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Items: 1 to 20 of 45

1.

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches.

Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF.

Nucleic Acids Res. 2006;34(20):5966-73. Epub 2006 Oct 26.

2.

Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching.

Gribskov M, Robinson NL.

Comput Chem. 1996 Mar;20(1):25-33.

PMID:
16718863
3.

Protein database searches using compositionally adjusted substitution matrices.

Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK.

FEBS J. 2005 Oct;272(20):5101-9. Review.

4.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Pruitt KD, Tatusova T, Maglott DR.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.

5.

GeneWise and Genomewise.

Birney E, Clamp M, Durbin R.

Genome Res. 2004 May;14(5):988-95.

6.

Versatile and open software for comparing large genomes.

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL.

Genome Biol. 2004;5(2):R12. Epub 2004 Jan 30.

7.

The compositional adjustment of amino acid substitution matrices.

Yu YK, Wootton JC, Altschul SF.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15688-93. Epub 2003 Dec 8.

8.

Fast algorithms for large-scale genome alignment and comparison.

Delcher AL, Phillippy A, Carlton J, Salzberg SL.

Nucleic Acids Res. 2002 Jun 1;30(11):2478-83.

9.

A new UAG-encoded residue in the structure of a methanogen methyltransferase.

Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK.

Science. 2002 May 24;296(5572):1462-6.

10.

BLAT--the BLAST-like alignment tool.

Kent WJ.

Genome Res. 2002 Apr;12(4):656-64.

11.
12.

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF.

Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. Review.

14.

FramePlus: aligning DNA to protein sequences.

Halperin E, Faigler S, Gill-More R.

Bioinformatics. 1999 Nov;15(11):867-73.

15.

Comparison of the complete protein sets of worm and yeast: orthology and divergence.

Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D.

Science. 1998 Dec 11;282(5396):2022-8. Review.

16.

Alignments without low-scoring regions.

Zhang Z, Berman P, Miller W.

J Comput Biol. 1998 Summer;5(2):197-210.

PMID:
9672828
17.

Translational readthrough in the hdc mRNA generates a novel branching inhibitor in the drosophila trachea.

Steneberg P, Englund C, Kronhamn J, Weaver TA, Samakovlis C.

Genes Dev. 1998 Apr 1;12(7):956-67.

18.

Empirical statistical estimates for sequence similarity searches.

Pearson WR.

J Mol Biol. 1998 Feb 13;276(1):71-84.

PMID:
9514730
19.

Comparison of DNA sequences with protein sequences.

Pearson WR, Wood T, Zhang Z, Miller W.

Genomics. 1997 Nov 15;46(1):24-36.

PMID:
9403055
20.

Aligning a DNA sequence with a protein sequence.

Zhang Z, Pearson WR, Miller W.

J Comput Biol. 1997 Fall;4(3):339-49.

PMID:
9278064
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