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Database of protein sequence alignments: PIR-ALN

G. Y. Srinivasarao, L.-S. L. Yeh, C. R. Marzec, B. C. Orcutt, W. C. Barker, F. Pfeiffer
<span title="1999-01-01">1999</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Protein Information Resource (PIR) has been maintaining a database of curated protein sequence alignments since 1991. The collection includes superfamily, family and homology domain alignments.  ...  The database has helped in classifying sequences, in defining new homology domains, and in spreading and standardizing protein names, features and keywords among members of a family or superfamily.  ...  The authors thank PIR staff for their contributions of alignments to the database and Katie Sidman and Desiree Goins for administrative support and help with Web page design.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.284">doi:10.1093/nar/27.1.284</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9847202">pmid:9847202</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC148157/">pmcid:PMC148157</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7zjhne6z6zewdldkcuu63lqynm">fatcat:7zjhne6z6zewdldkcuu63lqynm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070418053526/http://pir.georgetown.edu/pirwww/aboutpir/doc/narpiraln.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/46/14/461498cd0c818e890d208efd7e1177a92e0937dd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.284"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148157" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PIR-ALN: a database of protein sequence alignments

G. Y. Srinivasarao, L. S. Yeh, C. R. Marzec, B. C. Orcutt, W. C. Barker
<span title="1999-05-01">1999</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: The Protein Information Resource (PIR) maintains a database of annotated and curated alignments in order to visually represent interrelationships among sequences in the PIR-International Protein  ...  Results: Release 22.0, (December 1998), of the PIR-ALN database contains a total of 3806 alignments, including 1303 superfamily, 2131 family and 372 homology domain alignments.  ...  The authors thank PIR staff for their contributions of alignments to the database and Kathryn Sidman for administrative support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/15.5.382">doi:10.1093/bioinformatics/15.5.382</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10366659">pmid:10366659</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jv5js5zwfbgxbfqd6kd3szcx5i">fatcat:jv5js5zwfbgxbfqd6kd3szcx5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040830033953/http://bioinformatics.oupjournals.org:80/cgi/reprint/15/5/382.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5f/61/5f61889cda8de50a071369006a452099449562d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/15.5.382"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches

J. D. Thompson
<span title="2000-08-01">2000</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
DbClustal addresses the important problem of the automatic multiple alignment of the top scoring fulllength sequences detected by a database homology search.  ...  Local alignment information is incorporated into a ClustalW global alignment in the form of a list of anchor points between pairs of sequences.  ...  (15) also used ClustalW to generate multiple sequence alignments in the PIR-ALN database, followed by manual correction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.15.2919">doi:10.1093/nar/28.15.2919</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10908355">pmid:10908355</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC102675/">pmcid:PMC102675</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cc6w2wekvnbuzhxq4iz4hzmqte">fatcat:cc6w2wekvnbuzhxq4iz4hzmqte</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729143647/https://watermark.silverchair.com/282919.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaQwggGgBgkqhkiG9w0BBwagggGRMIIBjQIBADCCAYYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMUfNfFwha2EhbzYBCAgEQgIIBV6tbNB7jr8YxaKpicxSPaaZ8QyNJVaoDPua3_XtVegtToMx7zVg4zl7Daxqvtyn8WGldBtBmXrne3VZQCOJ_ySjTFj6gY3KLbV-cNIGmCeQe5f0e88yGyViBFJSn0wsZAXSBNvfB1KR-UYFQUZ8xxCYR8RchP-6wTWVt5wj7AjvvqBxVcX6CiZXz_CQ5lrGlqeREV9Ax9kld3X8XjO15TzzjQi6qtCqsw1hH3HSZSl4QXVx9E25-cL9AhappYIbIBt9AvoDp9cvpm6tg7ilcRR6kZaZwapUH68hIsviFKSs4D75b0ig2p_2AMyjW0hpF0TZFOOytzfrC_SG5QpkE9P_biOQ_qUmjNK890CkO7ZIYKTqXHNIfpOgOFxIZSQj2_pJHusXZ77t2gLdrKTaLmMe2m2-IGoAz4U0IxXYf8s_UnPMoBSMcD1expLpi7psJazcVnkpviQQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/e8/ace82bf7c4834643a9aa58920ecc6c97057c136c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.15.2919"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102675" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Alignment of Biological Sequences with Jalview [chapter]

James B. Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton, Lauren Lui, Anne Menard, Natasha Sherstnev, David Roldan-Martinez, Suzanne Duce, David M. A. Martin (+1 others)
<span title="2020-12-09">2020</span> <i title="Springer US"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments.  ...  and publication of alignments on the web.  ...  Development of the Jalview sequence analysis platform is coordinated at the University of Dundee with support from the UK's Biotechnology and Biological Sciences Research Council (BB/L010742/1), the Scottish  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-0716-1036-7_13">doi:10.1007/978-1-0716-1036-7_13</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33289895">pmid:33289895</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7116599/">pmcid:PMC7116599</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/skgegj4e2rdmhb2nm5gfcurew4">fatcat:skgegj4e2rdmhb2nm5gfcurew4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718073930/https://link.springer.com/content/pdf/10.1007%2F978-1-0716-1036-7_13.pdf?error=cookies_not_supported&amp;code=42dc64c3-0023-45e7-b9cb-89620bf02315" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/17/b0/17b0a3ce699106304ab19fb63c9f57f1dd42e7d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-0716-1036-7_13"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116599" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multiple sequence alignment with the Clustal series of programs

R. Chenna
<span title="2003-07-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees.  ...  The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs.  ...  T.K. would like to express his thanks to the Life Science Systems Division at Fujitsu Ltd for allowing him to participate in the bioinformatics research and development at the National Institute of Genetics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg500">doi:10.1093/nar/gkg500</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12824352">pmid:12824352</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC168907/">pmcid:PMC168907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/shatrsb3jnbaxelpjoaf5vm6ii">fatcat:shatrsb3jnbaxelpjoaf5vm6ii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730183853/https://watermark.silverchair.com/gkg500.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaAwggGcBgkqhkiG9w0BBwagggGNMIIBiQIBADCCAYIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM_kc-WdDotolazXeoAgEQgIIBUx6Ag32PZJMGdhVNTrknI-5w753gQH6oby2wp56j54suWooA9KDHnknbIBi6cu7NmokjelTwR-bGVE_636dpg596_QhZ6AhBP3LOl6AZbZSZKMQWj04KzDPNinDndZIqu2UnpVfSOR8Kn-rZJOO0QNmncvUNkpPIGCRkLe5GWumk6Er0er8vKdCtcErOnvlFyhtS2n0cB7hCn-lvq8mZVYUM8nsqyu35pJNT59Vs0hMjZnCWozYUmRQ0NHzZy0_B9fG-S3J53kwQoBE-aRuRvLwnNFwwT8MuCdKcgcy0-K9C8Tcx-6nN6FGQe5Ni2QFm31uHM2waQytlquMnr9zl6cN8WCCaduormsn6HD24InASlWsbcjGCdDjnB-c3Qe7wXVjNKHje4e0OvrXwa5L1tlAOaYTOysLwNaM_oFpyyPEcbFL5o3kiPwIlhff-UHB2Ha-t4w" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/9a/939a1b8461b0b4f0f533c4451ad3b1ad28f1131f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg500"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168907" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The PIR-International Protein Sequence Database

W. C. Barker, D. G. George, H.-W. Mewes, A. Tsugita
<span title="1992-05-11">1992</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The weekly release of the Protein Sequence Database can be accessed through the PIR Web site.  ...  The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available.  ...  PIR is a registered mark of the NBRF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/20.suppl.2023">doi:10.1093/nar/20.suppl.2023</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/1375994">pmid:1375994</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC333980/">pmcid:PMC333980</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pk66vyryyfb5vaugsej5ij3bna">fatcat:pk66vyryyfb5vaugsej5ij3bna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050312033754/http://pir.georgetown.edu:80/pirwww/aboutpir/doc/narpirpsd.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/cf/20cf582f9b1f4af1b61e5f880fd81a25050c05df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/20.suppl.2023"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC333980" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The PIR-International Protein Sequence Database

W. C. Barker, J. S. Garavelli, P. B. McGarvey, C. R. Marzec, B. C. Orcutt, G. Y. Srinivasarao, L.-S. L. Yeh, R. S. Ledley, H.-W. Mewes, F. Pfeiffer, A. Tsugita, C. Wu
<span title="1999-01-01">1999</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The weekly release of the Protein Sequence Database can be accessed through the PIR Web site.  ...  The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available.  ...  PIR is a registered mark of the NBRF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.39">doi:10.1093/nar/27.1.39</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9847137">pmid:9847137</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC148092/">pmcid:PMC148092</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uq7zz564e5f6vkhnb76u5t4wcy">fatcat:uq7zz564e5f6vkhnb76u5t4wcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050312033754/http://pir.georgetown.edu:80/pirwww/aboutpir/doc/narpirpsd.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/cf/20cf582f9b1f4af1b61e5f880fd81a25050c05df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.39"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148092" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

iProClass: an integrated, comprehensive and annotated protein classification database

C. H. Wu
<span title="2001-01-01">2001</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs.  ...  The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research.  ...  ACKNOWLEDGEMENTS This study is supported in part by grant DBI-9974855 from National Science Foundation, and grant P41 LM05798 from National Library of Medicine, NIH.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.52">doi:10.1093/nar/29.1.52</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11125047">pmid:11125047</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC29833/">pmcid:PMC29833</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bzntvv4tqzgafb52jdyvbp6ev4">fatcat:bzntvv4tqzgafb52jdyvbp6ev4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050306141258/http://pir.georgetown.edu:80/pirwww/aboutpir/doc/nar-iproclass-2001db.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7b/63/7b63bcb47e9825e51822e078847c43eae03cd033.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.52"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29833" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Protein Information Resource (PIR)

W. C. Barker
<span title="2000-01-01">2000</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases.  ...  The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration  ...  ACKNOWLEDGEMENTS PIR is a registered mark of NBRF. The work at NBRF is supported by grant number P41 LM05978 from the National Library of Medicine and by gifts from COMPAQ, Pfizer and Dupont.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.1.41">doi:10.1093/nar/28.1.41</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10592177">pmid:10592177</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC102418/">pmcid:PMC102418</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jmqdvezniratdgfskh5llytmua">fatcat:jmqdvezniratdgfskh5llytmua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808170848/http://www-nbrf.georgetown.edu/pirwww/aboutpir/doc/narpirpsd00.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/99/3f9977949774b56fd6051e1732036bfcd134e2f5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.1.41"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102418" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The PIR-International Protein Sequence Database

W. Barker
<span title="1998-01-01">1998</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
controlled, and well-organized protein sequence database.  ...  As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Library of Medicine. PIR is a registered mark of the NBRF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/26.1.27">doi:10.1093/nar/26.1.27</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9399794">pmid:9399794</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC147240/">pmcid:PMC147240</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mpbgtbyxa5bvvobxtyg2euuk6y">fatcat:mpbgtbyxa5bvvobxtyg2euuk6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050524020237/http://pir.georgetown.edu:80/pirwww/aboutpir/doc/narpirpsd98.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/af/0bafdf3f0e13df627f3c4bc971aafc7337e217cc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/26.1.27"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC147240" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The PIR-International Protein Sequence Database

D. George
<span title="1996-01-01">1996</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
controlled, and well-organized protein sequence database.  ...  As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Library of Medicine. PIR is a registered mark of the NBRF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/24.1.17">doi:10.1093/nar/24.1.17</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8594572">pmid:8594572</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC145575/">pmcid:PMC145575</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x24ghg3fnzd55cluciiwo33hbm">fatcat:x24ghg3fnzd55cluciiwo33hbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050524020237/http://pir.georgetown.edu:80/pirwww/aboutpir/doc/narpirpsd98.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/af/0bafdf3f0e13df627f3c4bc971aafc7337e217cc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/24.1.17"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC145575" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Progressive alignment using Shortest Common Supersequence

Ankush Garg, Deepak Garg
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3ezvnrqig5d5bmxdzmaqm4lk6e" style="color: black;">2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI)</a> </i> &nbsp;
Alignment of more than two sequences called multiple sequence alignment. Multiple sequence alignment solves many problems of bioinformatics. Multiple Sequence Alignment is an NP-hard problem.  ...  The complexity of finding the optimal alignment is O (L N ) where L is the length of the longest sequence and N is the number of sequences.  ...  Sequences are matched to a database of sequences and sequence are categorized according to the alignment scores with the sequences of database.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icacci.2014.6968310">doi:10.1109/icacci.2014.6968310</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/icacci/GargG14.html">dblp:conf/icacci/GargG14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fjx7bmzum5axjlagqc3zjxor3y">fatcat:fjx7bmzum5axjlagqc3zjxor3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809113345/http://www.gdeepak.com/thesisme/Progressive%20Alignment%20Using%20Shortest%20Common%20.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/57/e1576c9de8e9c1c5ea14a171f3e4f8cd7aebd187.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icacci.2014.6968310"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

ProClass Protein Family Database

C. H. Wu, S. Shivakumar, H. Huang
<span title="1999-01-01">1999</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The database currently consists of >155 000 sequence entries retrieved from both PIR-International and SWISS-PROT databases.  ...  ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns.  ...  To maximize family information retrieval, ProClass provides hypertext links to major family databases, including family and superfamily alignments [PIR-ALN (7) and ProtFam (8)], motif and domain databases  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.272">doi:10.1093/nar/27.1.272</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9847199">pmid:9847199</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC148154/">pmcid:PMC148154</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/447qhu5nbbf3nkozvg2rsdj6ry">fatcat:447qhu5nbbf3nkozvg2rsdj6ry</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809071625/http://pir.georgetown.edu/pirwww/aboutpir/doc/narproclass00.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/8e/d28e4648caf3612d0c5fd39bba2774ae7ff2e1ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/27.1.272"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148154" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ProClass protein family database

H. Huang
<span title="2000-01-01">2000</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The database currently consists of >155 000 sequence entries retrieved from both PIR-International and SWISS-PROT databases.  ...  ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns.  ...  To maximize family information retrieval, ProClass provides hypertext links to major family databases, including family and superfamily alignments [PIR-ALN (7) and ProtFam (8)], motif and domain databases  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.1.273">doi:10.1093/nar/28.1.273</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10592245">pmid:10592245</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC102450/">pmcid:PMC102450</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jip4gszgpbdn3eir46o5folofe">fatcat:jip4gszgpbdn3eir46o5folofe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809071625/http://pir.georgetown.edu/pirwww/aboutpir/doc/narproclass00.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/8e/d28e4648caf3612d0c5fd39bba2774ae7ff2e1ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/28.1.273"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102450" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The protein identification resource (PIR)

Kathryn E. Sidman, David G. George, Winona C. Barker, Lois T. Hunt
<span title="">1988</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Protein Identification Resource consists of an integrated computer system composed of a number of protein and nucleic acid sequence databases and software designed for the identification and analysis  ...  of protein sequences and their corresponding coding sequences.  ...  Inquiries regarding the services of the PIR should be directed to K.E. Sidman, Protein Identification Resource, at the above address. Prices subject to change. BITNET address: PIRMAILaGUNBRF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/16.5.1869">doi:10.1093/nar/16.5.1869</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/3353227">pmid:3353227</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC338183/">pmcid:PMC338183</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kb5jizjtwbcx7ikjkipneb35ju">fatcat:kb5jizjtwbcx7ikjkipneb35ju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207174440/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC338183&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/11/51/1151996d5db598b8afeb4991718ea72e1d723c2f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/16.5.1869"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC338183" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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