Literature DB >> 9021268

Methods for comparing a DNA sequence with a protein sequence.

X Huang1, J Zhang.   

Abstract

We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously process very huge sequences. The simplified versions of the methods were implemented as computer programs named NAP and LAP. The experimental results demonstrate that the programs are sensitive and powerful tools for finding genes by DNA-protein sequence homology.

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Year:  1996        PMID： 9021268     DOI： 10.1093/bioinformatics/12.6.497

Source DB:  PubMed          Journal:  Comput Appl Biosci        ISSN： 0266-7061


  26 in total

1.  Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome.

Authors:  Chris Upton; Stephanie Slack; Arwen L Hunter; Angelika Ehlers; Rachel L Roper
Journal:  J Virol       Date:  2003-07       Impact factor: 5.103

2.  Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity.

Authors:  Mark A Brockman; Denis R Chopera; Alex Olvera; Chanson J Brumme; Jennifer Sela; Tristan J Markle; Eric Martin; Jonathan M Carlson; Anh Q Le; Rachel McGovern; Peter K Cheung; Anthony D Kelleher; Heiko Jessen; Martin Markowitz; Eric Rosenberg; Nicole Frahm; Jorge Sanchez; Simon Mallal; Mina John; P Richard Harrigan; David Heckerman; Christian Brander; Bruce D Walker; Zabrina L Brumme
Journal:  J Virol       Date:  2012-04-11       Impact factor: 5.103

3.  An interactive bovine in silico SNP database (IBISS).

Authors:  Rachel J Hawken; Wesley C Barris; Sean M McWilliam; Brian P Dalrymple
Journal:  Mamm Genome       Date:  2004-10       Impact factor: 2.957

4.  Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C.

Authors:  Jaclyn K Wright; Vladimir Novitsky; Mark A Brockman; Zabrina L Brumme; Chanson J Brumme; Jonathan M Carlson; David Heckerman; Bingxia Wang; Elena Losina; Mopo Leshwedi; Mary van der Stok; Lungile Maphumulo; Nompumelelo Mkhwanazi; Fundisiwe Chonco; Philip J R Goulder; Max Essex; Bruce D Walker; Thumbi Ndung'u
Journal:  J Virol       Date:  2011-02-02       Impact factor: 5.103

5.  TransPS: A Transcriptome Post Scaffolding Method for Assembling High Quality Contigs.

Authors:  Mingming Liu; Zach N Adelman; Liqing Zhang
Journal:  Comput Biol J       Date:  2014-05-28

6.  Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

Authors:  Allison K Delong; Mingham Wu; Diane Bennett; Neil Parkin; Zhijin Wu; Joseph W Hogan; Rami Kantor
Journal:  AIDS Res Hum Retroviruses       Date:  2011-10-26       Impact factor: 2.205

7.  Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection.

Authors:  Mark A Brockman; Zabrina L Brumme; Chanson J Brumme; Toshiyuki Miura; Jennifer Sela; Pamela C Rosato; Carl M Kadie; Jonathan M Carlson; Tristan J Markle; Hendrik Streeck; Anthony D Kelleher; Martin Markowitz; Heiko Jessen; Eric Rosenberg; Marcus Altfeld; P Richard Harrigan; David Heckerman; Bruce D Walker; Todd M Allen
Journal:  J Virol       Date:  2010-09-01       Impact factor: 5.103

8.  Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters.

Authors:  Jaclyn K Wright; Zabrina L Brumme; Jonathan M Carlson; David Heckerman; Carl M Kadie; Chanson J Brumme; Bingxia Wang; Elena Losina; Toshiyuki Miura; Fundisiwe Chonco; Mary van der Stok; Zenele Mncube; Karen Bishop; Philip J R Goulder; Bruce D Walker; Mark A Brockman; Thumbi Ndung'u
Journal:  J Virol       Date:  2010-08-11       Impact factor: 5.103

Review 9.  Computational modeling of gene structure in Arabidopsis thaliana.

Authors:  Volker Brendel; Wei Zhu
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

10.  Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection.

Authors:  Zabrina L Brumme; Chanson J Brumme; Jonathan Carlson; Hendrik Streeck; Mina John; Quentin Eichbaum; Brian L Block; Brett Baker; Carl Kadie; Martin Markowitz; Heiko Jessen; Anthony D Kelleher; Eric Rosenberg; John Kaldor; Yuko Yuki; Mary Carrington; Todd M Allen; Simon Mallal; Marcus Altfeld; David Heckerman; Bruce D Walker
Journal:  J Virol       Date:  2008-07-09       Impact factor: 5.103
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