Literature DB >> 12761068

Zerg: a very fast BLAST parser library.

Apuã C M Paquola1, Abimael A Machado, Eduardo M Reis, Aline M Da Silva, Sergio Verjovski-Almeida.   

Abstract

SUMMARY: Zerg is a library of sub-routines that parses the output from all NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx) and returns the attributes of a BLAST report to the user. It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers. AVAILABILITY: http://bioinfo.iq.usp.br/zerg

Mesh：

Year:  2003        PMID： 12761068     DOI： 10.1093/bioinformatics/btg122

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

1.  Computational challenges in the analysis of ancient DNA.

Authors:  Kay Prüfer; Udo Stenzel; Michael Hofreiter; Svante Pääbo; Janet Kelso; Richard E Green
Journal:  Genome Biol       Date:  2010-05-06       Impact factor: 13.583

2.  Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni.

Authors:  Ricardo DeMarco; Andre T Kowaltowski; Abimael A Machado; M Bento Soares; Cybele Gargioni; Toshie Kawano; Vanderlei Rodrigues; Alda M B N Madeira; R Alan Wilson; Carlos F M Menck; João C Setubal; Emmanuel Dias-Neto; Luciana C C Leite; Sergio Verjovski-Almeida
Journal:  J Virol       Date:  2004-03       Impact factor: 5.103

3.  The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

Authors:  Massimiliano Orsini; Simone Carcangiu; Gianmauro Cuccuru; Paolo Uva; Anna Tramontano
Journal:  PLoS One       Date:  2013-05-07       Impact factor: 3.240

4.  BlaSTorage: a fast package to parse, manage and store BLAST results.

Authors:  Massimiliano Orsini; Simone Carcangiu
Journal:  Source Code Biol Med       Date:  2013-01-30

5.  Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions.

Authors:  Thiago M Venancio; Ricardo DeMarco; Giulliana T Almeida; Katia C Oliveira; João C Setubal; Sergio Verjovski-Almeida
Journal:  BMC Genomics       Date:  2007-11-08       Impact factor: 3.969

6.  BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data.

Authors:  Ralf Stefan Neumann; Surendra Kumar; Thomas Hendricus Augustus Haverkamp; Kamran Shalchian-Tabrizi
Journal:  BMC Bioinformatics       Date:  2014-05-05       Impact factor: 3.169
  6 in total

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