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The SSAHA trace server
Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.
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Matching seeds of a few kmer words are detected by the SSAHA algorithm. ...
We present a client/server database system with the potential to make all DNA sequences searchable. ...
Acknowledgement We would like to thank Professor Phil Green, University of Washington, who has kindly agreed for the use of Phrap/Cross_Match package for sequence alignment in the SSAHA system. ...
doi:10.1109/csb.2004.1332490
dblp:conf/csb/NingSSLRC04
fatcat:k52nzqxihzdchdviwsgc4mka7q
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives
2002
Bioinformatics
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GENOTRACE identifies the genomic organization for a cDNA using raw data from genome sequencing projects in progress (trace archives). ...
Availability: The package and examples of output files can be downloaded from http://rat.niob.knaw.nl/ GENOTRACE Contact: ecuppen@niob.knaw.nl ...
ACKNOWLEDGEMENTS
This research was financially supported by the Dutch Ministry of Economic Affairs through the Innovation Oriented Research Program on Genomics ...
doi:10.1093/bioinformatics/18.10.1396
pmid:12376385
fatcat:ejodff4pizg5tgdwfek5sagxam
SSAHA: A Fast Search Method for Large DNA Databases
2001
Genome Research
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Jaak Vilo of the European Bioinformatics Institute for his insightful comments regarding sorting algorithms. The publication costs of this article were defrayed in part by payment of page charges. ...
The Ensembl project (see http://www.ensembl.org) features a Web server that allows users to conduct SSAHA searches of both the latest GoldenPath assembly of the human genome and the Ensembl Trace Repository ...
However, for many applications (such as the Ensembl SSAHA server) it is more flexible to retain all occurrences of all words and implement the cutoff threshold N in software. ...
doi:10.1101/gr.194201
pmid:11591649
pmcid:PMC311141
fatcat:bozz7dn7c5fvho7uinzkbafequ
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes
2008
Computer applications in the biosciences : CABIOS
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mapping server which aligns them to an Ensembl genome. ...
Taking linker based sequences as input, iMapper scans and trims the sequence to remove the linker and sequences derived from the insertional mutagen. ...
genomic junction fragments of on average 200 bp in length the optimal SSAHA score is 35. ...
doi:10.1093/bioinformatics/btn541
pmid:18974167
pmcid:PMC2639305
fatcat:xg7rtddn5bbljixaum6ep53e4q
Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
2004
Genome Research
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We used the stand-alone version of SIFT and queried the PolyPhen server remotely. ...
The increased performance of the SSAHA search algorithm allowed us to compare raw WGS sequence data (∼13 ן 10 9 bp) against mRNA and EST sequences. ...
Local SSAHA search was performed to collect hits with nearly exact homology containing a single mismatch in the mRNA/EST subset and remote search (using Ensembl SSAHA search server) in case of mRNA/EST ...
doi:10.1101/gr.2154304
pmid:15231757
pmcid:PMC442160
fatcat:p3bj2szbsngclkqxt54bbkuhmm
The Ensembl genome database project
2002
Nucleic Acids Research
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The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. ...
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. ...
The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL. ...
doi:10.1093/nar/30.1.38
pmid:11752248
pmcid:PMC99161
fatcat:u2fj5iq6tfga7kj7xrc3bk3su4
Tracembler – software for in-silico chromosome walking in unassembled genomes
2007
BMC Bioinformatics
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In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. ...
We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly ...
QD is currently supported by the Indiana METACyt Initiative, funded by the Lilly Endowment, Inc. We are grateful for constructive suggestions from two anonymous reviewers. ...
doi:10.1186/1471-2105-8-151
pmid:17490482
pmcid:PMC1876249
fatcat:odytnkgyazbv3pwtyjlk5qmyjy
Modern BLAST Programs
[chapter]
2010
Problem Solving Handbook in Computational Biology and Bioinformatics
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The Basic Local Alignment Search Tool (BLAST) is arguably the most widely used program in bioinformatics. ...
This chapter surveys the development of BLAST and BLAST-like programs for homology search, alignment statistics that are used in assessment of reported matches in BLAST, and provides the reader with guidance ...
McGinnis for discussion of the implementation issues of BLAST programs. ...
doi:10.1007/978-0-387-09760-2_1
fatcat:ismdnrwirjb57elsfb54z36gqq
Survey on index based homology search algorithms
2007
Journal of Supercomputing
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Based on the classification, the characteristics of the currently popular index based homology search algorithms are compared and analyzed. ...
The paper briefly introduces main index construction methods. ...
The authors thank Professor Dominique Lavenier for his valuable suggestions on this paper, and also thank anonymous reviewers for their comments to improve the readability of this paper. ...
doi:10.1007/s11227-006-0041-0
fatcat:hhijz2rah5a5jcbu4d6ecj3npi
Genetic variation in the zebrafish
2006
Genome Research
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Furthermore, the number of haplotypes per locus is relatively large, reflecting independent establishment of the different lines from wild isolates. ...
The analysis reveals very high nucleotide diversity between zebrafish isolates. ...
Louis, and Agencourt Bioscience Corporation for providing zebrafish EST sequence and/or quality data, and the Zebrafish Sequencing Group at the Wellcome Trust Sanger Institute for making the WGS trace ...
doi:10.1101/gr.4791006
pmid:16533913
pmcid:PMC1457036
fatcat:5giczdlbznhzrel5nj5r5wieea
The Vertebrate Genome Annotation (Vega) database
2004
Nucleic Acids Research
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In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. ...
Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions. ...
We thank the Ensembl Project for the software that is the basis of the Vega website and the Otter client/server system and the Glovar project for providing support for SNPs on Vega. ...
doi:10.1093/nar/gki135
pmid:15608237
pmcid:PMC540089
fatcat:isoio6kzqvh3tilxim6eqczvqu
PASH 2.0: SCALEABLE SEQUENCE ANCHORING FOR NEXT-GENERATION SEQUENCING TECHNOLOGIES
2007
Biocomputing 2008
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We obtained about 16 million Sanger
reads from fosmid end sequences in the NCBI Trace Archive, for a total of
7,946,887 mate pairs, and anchored them onto the human genome with Blat and
Pash 2.0. ...
We used
Pash 2.0, and BLAT Client/Server version 32. All experiments were run
sequentially; when input was split in multiple chunks, we reported total compute
time. ...
doi:10.1142/9789812776136_0012
fatcat:dyf4gemuhbg3tcaowukju63yrm
2008 BBSRC Tools and Resources Development Fund Application - pubmed2ensembl: a resource for linking biological literature to genome sequences
2012
Figshare
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In contrast to Entrez Gene, we will preserve the original data source so that users can trace the provenance of the curated data. ...
We will establish a dedicated server to run the pubmed2ensembl database and query interfaces. ...
doi:10.6084/m9.figshare.94137.v2
fatcat:63oszpocifezhoznpqvjc4nn3i
An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms
2007
Comparative and Functional Genomics
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In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. ...
At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors ...
ACKNOWLEDGMENT The authors gratefully acknowledge financial support through the Generation Challenge Program for the high performance computing facility and software tools development. ...
doi:10.1155/2007/35604
pmid:18273384
pmcid:PMC2216057
fatcat:yydzov5fibcfdklsf6qz6xrxdq
biobambam: tools for read pair collation based algorithms on BAM files
2014
Source Code for Biology and Medicine
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of variants between the mapped data and the reference or of variants within the mapped data. ...
of the pairs. ...
Acknowledgements GT and SL are supported by the Wellcome Trust. ...
doi:10.1186/1751-0473-9-13
pmcid:PMC4075596
fatcat:gjvnaljkyrfljfgxpl6qxpdycq
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