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The SSAHA trace server

Zemin Ning, W. Spooner, A. Spargo, S. Leonard, M. Rae, A. Cox
Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.  
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

E. Berezikov, R. H.A. Plasterk, E. Cuppen
2002 Bioinformatics  
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

Z. Ning
2001 Genome Research  
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

Jun Kong, Fei Zhu, Jim Stalker, David J. Adams
2008 Computer applications in the biosciences : CABIOS  
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

V. Guryev
2004 Genome Research  
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

T. Hubbard
2002 Nucleic Acids Research  
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

Qunfeng Dong, Matthew D Wilkerson, Volker Brendel
2007 BMC Bioinformatics  
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]

Jian Ma, Louxin Zhang
2010 Problem Solving Handbook in Computational Biology and Bioinformatics  
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

Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
2007 Journal of Supercomputing  
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

V. Guryev
2006 Genome Research  
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

J. L. Ashurst
2004 Nucleic Acids Research  
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

CRISTIAN COARFA, ALEKSANDAR MILOSAVLJEVIC
2007 Biocomputing 2008  
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

Casey Bergman, Goran Nenadic
2012 Figshare  
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

B. Jayashree, Manindra S. Hanspal, Rajgopal Srinivasan, R. Vigneshwaran, Rajeev K. Varshney, N. Spurthi, K. Eshwar, N. Ramesh, S. Chandra, David A. Hoisington
2007 Comparative and Functional Genomics  
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

German Tischler, Steven Leonard
2014 Source Code for Biology and Medicine  
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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