-
1
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared-by mutiple proteomes
-
Alexeyenko,A. et al. (2006) Automatic clustering of orthologs and inparalogs shared-by mutiple proteomes. Bioinformatics, 22, e9-e15.
-
(2006)
Bioinformatics
, vol.22
-
-
Alexeyenko, A.1
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
4
-
-
0035875343
-
GeneMarkS: A self-training method for prediction of gone starts in microbial genomes implications for finding sequence motifs in regulatory regions
-
Besemer,J. et al. (2001) GeneMarkS: A self-training method for prediction of gone starts in microbial genomes implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29 2607-2618.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2607-2618
-
-
Besemer, J.1
-
5
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner,F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
-
6
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBE in 2003
-
Boeckmann,B. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBE in 2003. Nucleic Acids Res., 31, 365-370.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
-
7
-
-
0032491377
-
Predicting function: From genes to genomes and back
-
Bork,P. et al. (1998) Predicting function: From genes to genomes and back. J. Mol. Biol., 283, 707-725.
-
(1998)
J. Mol. Biol
, vol.283
, pp. 707-725
-
-
Bork, P.1
-
8
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
Brenner,S.E. et al. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA, 95, 6073-6078.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
-
9
-
-
33747817416
-
Roundup: A multi-genome repository of orthologs and evolutionary distances
-
Deluca,T.F. et al. (2006) Roundup: A multi-genome repository of orthologs and evolutionary distances. Bioinformatics, 22, 2044-2046.
-
(2006)
Bioinformatics
, vol.22
, pp. 2044-2046
-
-
Deluca, T.F.1
-
10
-
-
3042739661
-
What is dynamic programming?
-
Eddy,S.R. (2004) What is dynamic programming? Nat. biotechnol., 22, 909-910.
-
(2004)
Nat. biotechnol
, vol.22
, pp. 909-910
-
-
Eddy, S.R.1
-
11
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch,W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
-
(2000)
Trends Genet
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
12
-
-
20044369186
-
An adaptive radiation model for the origin of new gene functions
-
Francino,M.P. (2005) An adaptive radiation model for the origin of new gene functions. Nat. Genet., 37, 573-577.
-
(2005)
Nat. Genet
, vol.37
, pp. 573-577
-
-
Francino, M.P.1
-
13
-
-
33746755926
-
Improving the specificity of high-throughput ortholog prediction
-
Fulton,D.L. et al. (2006) Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics, 7, 270.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 270
-
-
Fulton, D.L.1
-
14
-
-
0042423439
-
Automated annotation of microbial proteomes in SWISS-PROT
-
Gattiker,A. et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem., 27, 49-58.
-
(2003)
Comput. Biol. Chem
, vol.27
, pp. 49-58
-
-
Gattiker, A.1
-
15
-
-
6044261571
-
Conservation of adjacency as evidence of paralogous operons
-
Janga,S.C. and Moreno-Hagelsieb,G. (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res., 32, 5392-5397.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5392-5397
-
-
Janga, S.C.1
Moreno-Hagelsieb, G.2
-
16
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski,L.B. and Golding,G.B. (2001) The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol., 52, 540-542.
-
(2001)
J. Mol. Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
17
-
-
0033965854
-
NCBI's LocusLink and RefSeq
-
Maglott,D.R. et al. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 126-128
-
-
Maglott, D.R.1
-
18
-
-
0001291140
-
A powerful non-homology method for the prediction of operons in prokaryotes
-
Moreno-Hagelsieb,G. and Collado-Vides,J. (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 (Suppl. 1), S329-S336.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Moreno-Hagelsieb, G.1
Collado-Vides, J.2
-
20
-
-
0034764340
-
Having a BLAST with bioinformatics (and avoiding BLASTphenry)
-
REVIEWS2002
-
Pertsemlidis,A. and Fondon,J.W.3rd (2001) Having a BLAST with bioinformatics (and avoiding BLASTphenry). Genome Biol., 2 REVIEWS2002.
-
(2001)
Genome Biol
, vol.2
-
-
Pertsemlidis, A.1
Fondon 3rd, J.W.2
-
21
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Database Issue, D501-D504
-
Pruitt,K.D. et al. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33 (Database Issue), D501-D504.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Pruitt, K.D.1
-
22
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer,A.A. et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
-
23
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1981)
J. Mol. Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
24
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov,R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
-
25
-
-
0042902833
-
The cog database: An update version includes eukaryotes
-
Tatusov,R.L. et al. (2003) The cog database: An update version includes eukaryotes. BMC Bioinformatics, 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
-
26
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
-
27
-
-
33846086800
-
recent developments in the integration and prediction of protein interactions
-
Database issue, D358-D362, STRING 7
-
von Mering,C. et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res., 35 (Database issue), D358-D362.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
-
28
-
-
0141626909
-
(1003) Detecting putative orthologs
-
Wall,D.P. et al. (1003) Detecting putative orthologs. Bioinformatics, 19, 1710-1711.
-
(1710)
Bioinformatics
, vol.19
-
-
Wall, D.P.1
-
29
-
-
0030683599
-
PAML: A program package for phylogenac analysis by maximum likelihood
-
Yang,Z. (1997) PAML: A program package for phylogenac analysis by maximum likelihood. Comput. Appl. Biosci., 13, 555-556.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
30
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang,Z. (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
|