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EXACT ALGORITHMS FOR COMPUTING PAIRWISE ALIGNMENTS AND 3-MEDIANS FROM STRUCTURE-ANNOTATED SEQUENCES (EXTENDED ABSTRACT)
2000
Biocomputing 2001
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Ø ÓÒ × Ì Ñ Ò´Ì ½ · Û × Ì ½ · Û × ´½µ Ì ½ ½ · Û´Ë ½ Ë ¾ µµ Ì × Ð ÙÐ Ø ÓÒ × Ú Ö Û Ò Ö Ò ÔÓ ÒØ× Ö Ò ÓÙÒØ Ö × ÓÐÐÓÛ× ½º Ï Ò Ò Ò Ø Ð Ö Ò ÔÓ ÒØ × Ò ÓÙÒØ Ö ¸ ÓØ Ø Ð × Ö Ð Ø Ú ØÓ Ø Ø Ð Ò ÓÒ× Ö Ø Ø Ò ÐÙ Ø Ø Ö ³× ...
ÔÖÓÔÓÖØ ÓÒ Ð ØÓ Ø ÒÙÑ Ö Ó Ð Ú ×´Ð Ò Ø Ó Ø ×Ù ×ØÖ Ò ¸Ð µº Ë Ò Ø × ÕÙ Ò × Ñ Ý Ú « Ö ÒØ Ò ÙÑ Ö× Ó Ð Ú Ð׸ ÒÝ Ø ×Ø Ò ÓÖ Ð ÒÑ ÒØ Ð ÓÖ Ø Ñ × ÓÙÐ ÐÐÓÛ Ð Ú Ð× ØÓ ÝÔ ×× ´Û Ø Ô Ò ÐØ × ÓÖ Ø Ö ÑÓÚ ÐÓ Ø Ñ Ø ×Ù ØÖ ³× ...
doi:10.1142/9789814447362_0054
fatcat:5ruchx77jnedza57h3j2fxy7eq
Lightweight comparison of RNAs based on exact sequence–structure matches
2009
Computer applications in the biosciences : CABIOS
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Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method ExpaRNA (exact pattern of alignment of RNA) computes the longest collinear ...
sequence of substructures common to two RNAs in O(H ·nm) time and O(nm) space, where H n·m for real RNA structures. ...
In addition, we explain how sequence-structure alignment methods can profit from anchor constraints. Sections 3 and 4 present the results for two applications of our tool ExpaRNA. ...
doi:10.1093/bioinformatics/btp065
pmid:19189979
pmcid:PMC2722993
fatcat:klmuwxxs6vawlj7p5cvojtmib4
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
2012
Bioinformatics
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annotation into the future despite rapidly expanding databases. ...
Sequence similarity searching followed by k-nearest neighbor classification is the most widely used tool to predict the function or structure of anonymous gene products that come out of genome sequencing ...
ACKNOWLEDGEMENT The authors thank Pasi Korhonen and Kimmo Mattila for technical assistance. Funding: Biocentrum Helsinki. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/bts417
pmid:22962464
pmcid:PMC3436844
fatcat:v2ivfdvfynf6fpl3ucxpo5o6xe
A strategy for assembling the maize (Zea mays L.) genome
2004
Bioinformatics
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Algorithmic innovations are used to reduce the number of pairwise alignments significantly without sacrificing quality. ...
Traditional assembly programs are inadequate for this approach because they are optimized for a uniform sampling of the genome and inherently lack the ability to differentiate highly similar paralogs. ...
Methods
Input data, masking of low quality and contaminant sequences Zea mays genomic survey sequences (GSSs) from the inbred line B73 Fig. 3 . ...
doi:10.1093/bioinformatics/bth017
pmid:14734303
fatcat:kuw5qp4wubgsjbc3hmhx2glysq
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation
[article]
2020
arXiv
pre-print
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We present AnySeq - a novel library for computing different types of pairwise alignments of DNA sequences. ...
Using the AnyDSL compiler framework, AnySeq enables the compilation of algorithmic variants that are highly optimized for specific usage scenarios and hardware targets with a single, uniform codebase. ...
For pairwise alignment computation, the Smith-Waterman algorithm [1] , the Needleman-Wunsch algorithm [2] , and their variants are widely used. ...
arXiv:2002.04561v1
fatcat:lbu6ikpes5hgrnprknn2fwlldq
Multi-Part Pattern Analysis: Combining Structure Analysis And Source Separation To Discover Intra-Part Repeated Sequences
2017
Zenodo
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[TODO] Add abstract here. ...
(For a comparison of structure evaluation metrics, see [16] .) However, the rows of A and E are not necessarily aligned in the correct order. ...
The procedure for this is similar to our analysis algorithm (see Fig. 3 ). ...
doi:10.5281/zenodo.1417685
fatcat:rt4ndl2vuzfq5irz53vw7rarmy
PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks
2021
Frontiers in Bioinformatics
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At the same time, computational analysis is widely used for protein annotation, but a dearth of experimental verification has contributed to inaccurate annotation as well as to annotation error propagation ...
and a query-able webpage where the FASTA headers of sequences from the cluster best matching an input sequence are returned. ...
sequence alignment, and semi-global sequence alignment algorithms. ...
doi:10.3389/fbinf.2021.749008
fatcat:64pixdq3rfeq3pm4qv7bei3hjy
MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale
[article]
2020
bioRxiv
pre-print
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MetaGraph provides a flexible methodological framework allowing for index construction to be scaled from consumer laptops to distribution onto a cloud compute cluster for processing terabases to petabases ...
Besides demonstrating the utility of MetaGraph indexes on key applications, such as experiment discovery, sequence alignment, error correction, and differential assembly, we make a wide range of indexes ...
and Genome Annotation" as part of Swiss National Research Programme (NRP) 75 "Big Data." ...
doi:10.1101/2020.10.01.322164
fatcat:md5ipa2rlnh4fky57su46ym7ey
Generic Model Abstraction from Examples
[chapter]
2002
Lecture Notes in Computer Science
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Moreover, since the presence of texture and surface markings seriously affected the computational complexity of these systems, they too selected objects which were texture-free -objects for which a salient ...
This was accomplished by removing object surface markings and structural detail, controlling lighting conditions, and reducing scene clutter. ...
The authors would like to thank Allan Jepson for his insightful comments and feedback on this work, as well as the three reviewers, whose comments have improved the presentation. ...
doi:10.1007/3-540-45993-6_1
fatcat:sfhn5cdxtzhzjlhxtldeomz7py
Generic model abstraction from examples
2005
IEEE Transactions on Pattern Analysis and Machine Intelligence
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Moreover, since the presence of texture and surface markings seriously affected the computational complexity of these systems, they too selected objects which were texture-free -objects for which a salient ...
This was accomplished by removing object surface markings and structural detail, controlling lighting conditions, and reducing scene clutter. ...
The authors would like to thank Allan Jepson for his insightful comments and feedback on this work, as well as the three reviewers, whose comments have improved the presentation. ...
doi:10.1109/tpami.2005.139
pmid:16013760
fatcat:ac6ffqylwjbptfftcp4nuotdfm
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
2007
Genome Research
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Acknowledgments We thank Bret Pearson for the cloning of the 31 S. mediterranea mRNAs discussed in the Results section. This work was supported in part by NIH grant K22-HG0064 to I.K. ...
Note too the 3Ј UTR on the MAKER annotation derived from the EST alignments. The MAKER mRNA quality index Compute data are essential for discriminating real genes from false positives. ...
MAKER therefore uses Exonerate (Slater and Birney 2005) , a splice-site aware alignment algorithm to realign, or polish, sequences following filtering and clustering (see steps 2 and 3, below). ...
doi:10.1101/gr.6743907
pmid:18025269
pmcid:PMC2134774
fatcat:3x6s4qg33ngedo3ypwcsnbst34
Fine-grained annotation and classification of de novo predicted LTR retrotransposons
2009
Nucleic Acids Research
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For further analysis, it is desirable to obtain an annotation of the internal structure of such candidates. ...
It uses local alignment and hidden Markov modelbased algorithms to detect retrotransposonassociated protein domains as well as primer binding sites and polypurine tracts. ...
ACKNOWLEDGEMENTS The authors would like to thank Jan Sellmann for largescale testing of LTRdigest and providing valuable bug reports as well as helpful suggestions for usability improvement. ...
doi:10.1093/nar/gkp759
pmid:19786494
pmcid:PMC2790888
fatcat:26zke6pvaveirdkjvdcc2zxv7m
Cognition-Inspired Descriptors For Scalable Cover Song Retrieval
2014
Zenodo
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[TODO] Add abstract here. ...
Multiple Sequence Alignment MSA is a bioinformatics method that extends pairwise alignment of symbolic arrays to a higher number of sequences [4] . ...
Whenever two sequences are aligned, a consensus can be computed, which can be used for the alignment connecting the two sequences to the rest of the three. ...
doi:10.5281/zenodo.1417794
fatcat:66ty7oeizrb7zg5figltmhqag4
Widespread purifying selection on RNA structure in mammals
2013
Nucleic Acids Research
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The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens ...
We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. ...
ACKNOWLEDGEMENTS The authors thank Dr Gerald Hartig and the University of Queensland/Queensland Parallel Supercomputing Foundation (UQ/QPSF) for their assistance with the high-performance computing infrastructure ...
doi:10.1093/nar/gkt596
pmid:23847102
pmcid:PMC3783177
fatcat:cxfxvqsu2fcclczffkpdyhkmsy
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
2007
BMC Bioinformatics
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Acknowledgements: This work is funded by an RO1 from the NHGRI and by a Presidential Early Career Award for Scientists and Engineers from the National Science Foundation. ...
For comparison, we also computed the classification rate achieved with ranks computed using FASTA [5] , (a sequence-alignment program), CE [6] (a structure alignment program), SCOP [4] (a structural ...
Detailed results will be reported in an extended version of this abstract. ...
doi:10.1186/1471-2105-8-s4-s4
pmid:17570147
pmcid:PMC1892083
fatcat:o5p5c46emzbhxlmq27vqibskdi
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