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EXACT ALGORITHMS FOR COMPUTING PAIRWISE ALIGNMENTS AND 3-MEDIANS FROM STRUCTURE-ANNOTATED SEQUENCES (EXTENDED ABSTRACT)

P. A. EVANS, H. T. WAREHAM
2000 Biocomputing 2001  
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

Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen
2009 Computer applications in the biosciences : CABIOS  
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

J. P. Koskinen, L. Holm
2012 Bioinformatics  
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

S. J. Emrich, S. Aluru, Y. Fu, T.-J. Wen, M. Narayanan, L. Guo, D. A. Ashlock, P. S. Schnable
2004 Bioinformatics  
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]

André Müller , Richard Membarth , Sebastian Hack Saarland University)
2020 arXiv   pre-print
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

Jordan B. L. Smith, Masataka Goto
2017 Zenodo  
[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

Jin Tao, Kelly A. Brayton, Shira L. Broschat
2021 Frontiers in Bioinformatics  
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]

Mikhail Karasikov, Harun Mustafa, Daniel Danciu, Marc Zimmermann, Christopher Barber, Gunnar Ratsch, Andre Kahles
2020 bioRxiv   pre-print
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]

Yakov Keselman, Sven Dickinson
2002 Lecture Notes in Computer Science  
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

Y. Keselman, S. Dickinson
2005 IEEE Transactions on Pattern Analysis and Machine Intelligence  
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

B. L. Cantarel, I. Korf, S. M.C. Robb, G. Parra, E. Ross, B. Moore, C. Holt, A. Sanchez Alvarado, M. Yandell
2007 Genome Research  
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

Sascha Steinbiss, Ute Willhoeft, Gordon Gremme, Stefan Kurtz
2009 Nucleic Acids Research  
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

Jan Van Balen, Dimitrios Bountouridis, Frans Wiering, Remco C. Veltkamp
2014 Zenodo  
[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

Martin A. Smith, Tanja Gesell, Peter F. Stadler, John S. Mattick
2013 Nucleic Acids Research  
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

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2007 BMC Bioinformatics  
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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