Literature DB >> 14668240

PRIMEX: rapid identification of oligonucleotide matches in whole genomes.

Matej Lexa1, Giorgio Valle.   

Abstract

SUMMARY: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools. AVAILABILITY: Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex

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Year:  2003        PMID： 14668240     DOI： 10.1093/bioinformatics/btg350

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


  9 in total

1.  Stability of the T-DNA flanking regions in transgenic Arabidopsis thaliana plants under influence of abiotic stress and cultivation practices.

Authors:  Nina Papazova; Rim Ghedira; Sabine Van Glabeke; Aghleb Bartegi; Pieter Windels; Isabel Taverniers; Isabel Roldan-Ruiz; Erik Van Bockstaele; Anne Milcamps; Guy Van Den Eede; Ann Depicker; Marc De Loose
Journal:  Plant Cell Rep       Date:  2007-12-18       Impact factor: 4.570

2.  DomSVR: domain boundary prediction with support vector regression from sequence information alone.

Authors:  Peng Chen; Chunmei Liu; Legand Burge; Jinyan Li; Mahmood Mohammad; William Southerland; Clay Gloster; Bing Wang
Journal:  Amino Acids       Date:  2010-02-18       Impact factor: 3.520

3.  GenoMass--a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests.

Authors:  Qing Liao; Chang Shen; Paul Vouros
Journal:  J Mass Spectrom       Date:  2009-04       Impact factor: 1.982

4.  MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.

Authors:  Wubin Qu; Yang Zhou; Yanchun Zhang; Yiming Lu; Xiaolei Wang; Dongsheng Zhao; Yi Yang; Chenggang Zhang
Journal:  Nucleic Acids Res       Date:  2012-06-11       Impact factor: 16.971

5.  GENOMEMASKER package for designing unique genomic PCR primers.

Authors:  Reidar Andreson; Eric Reppo; Lauris Kaplinski; Maido Remm
Journal:  BMC Bioinformatics       Date:  2006-03-27       Impact factor: 3.169

6.  Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates.

Authors:  Youfang Cao; Lianjie Wang; Kexue Xu; Chunhai Kou; Yulei Zhang; Guifang Wei; Junjian He; Yunfang Wang; Liping Zhao
Journal:  BMC Bioinformatics       Date:  2005-07-26       Impact factor: 3.169

7.  KemaDom: a web server for domain prediction using kernel machine with local context.

Authors:  Lusheng Chen; Wei Wang; Shaoping Ling; Caiyan Jia; Fei Wang
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

8.  Improved assay-dependent searching of nucleic acid sequence databases.

Authors:  Jason D Gans; Murray Wolinsky
Journal:  Nucleic Acids Res       Date:  2008-05-31       Impact factor: 16.971

Review 9.  Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine.

Authors:  Hao Ye; Joe Meehan; Weida Tong; Huixiao Hong
Journal:  Pharmaceutics       Date:  2015-11-23       Impact factor: 6.321
  9 in total

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