-
1
-
-
24644485994
-
JIGSAW: Integration of multiple sources of evidence for gene prediction
-
Allen,J.E. and Salzberg,S.L. (2005) JIGSAW: Integration of multiple sources of evidence for gene prediction. Bioinformatics, 21, 3596-3603.
-
(2005)
Bioinformatics
, vol.21
, pp. 3596-3603
-
-
Allen, J.E.1
Salzberg, S.L.2
-
2
-
-
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
-
3
-
-
0030628597
-
Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison
-
Birney,E. and Durbin,R. (1997) Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. ISMB, 5, 56-64.
-
(1997)
ISMB
, vol.5
, pp. 56-64
-
-
Birney, E.1
Durbin, R.2
-
4
-
-
2442713832
-
GeneWise and genomewise
-
Birney,E. et al. (2004) GeneWise and genomewise. Genome Res. 14, 988-995.
-
(2004)
Genome Res
, vol.14
, pp. 988-995
-
-
Birney, E.1
-
5
-
-
0029056051
-
Detection of new genes in a bacterial genome using Markov models for three gene classes
-
Borodovsky,M. et al. (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res. 23, 3554-3562.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 3554-3562
-
-
Borodovsky, M.1
-
6
-
-
29144445262
-
ExonHunter: A comprehensive approach to gene finding
-
Brejova,B. et al. (2005) ExonHunter: A comprehensive approach to gene finding. Bioinformatics, 21 (Suppl. 1), i57-i65.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Brejova, B.1
-
7
-
-
19944414942
-
Optimizing multiple seeds for protein homology search
-
Brown,D.G. (2005) Optimizing multiple seeds for protein homology search. IEEE/ACM Trans. Comput. Biol. Bioinform., 2, 29-38.
-
(2005)
IEEE/ACM Trans. Comput. Biol. Bioinform
, vol.2
, pp. 29-38
-
-
Brown, D.G.1
-
8
-
-
0030585734
-
Evaluation of gene structure prediction programs
-
Burset,M. and Guigo,R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
-
(1996)
Genomics
, vol.34
, pp. 353-367
-
-
Burset, M.1
Guigo, R.2
-
9
-
-
0036677673
-
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
-
Cannata,N. et al. (2002) Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. Bioinformatics, 18, 1102-1108.
-
(2002)
Bioinformatics
, vol.18
, pp. 1102-1108
-
-
Cannata, N.1
-
10
-
-
34347389905
-
Three distinct modes of intron dynamics in the evolution of eukaryotes
-
Carmel,L. et al. (2007) Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res., 17, 1034-1044.
-
(2007)
Genome Res
, vol.17
, pp. 1034-1044
-
-
Carmel, L.1
-
11
-
-
33745051802
-
Reference based annotation with GeneMapper
-
Chatterji,S. and Pachter,L. (2006) Reference based annotation with GeneMapper. Genome Biol., 7, R29.
-
(2006)
Genome Biol
, vol.7
-
-
Chatterji, S.1
Pachter, L.2
-
12
-
-
3843113189
-
Origins of recently gained introns in Caenorhabditis
-
Coghlan,A. andWolfe,K.H. (2004) Origins of recently gained introns in Caenorhabditis. Proc. Natl Acad. Sci. USA, 101, 11362-11367.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 11362-11367
-
-
Coghlan, A.1
andWolfe, K.H.2
-
13
-
-
34547852257
-
Homology search for genes
-
Cui,X. et al. (2007) Homology search for genes. Bioinformatics 23, i97-i103.
-
(2007)
Bioinformatics
, vol.23
-
-
Cui, X.1
-
14
-
-
2442707676
-
The Ensembl automatic gene annotation system
-
Curwen,V. et al. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
-
(2004)
Genome Res
, vol.14
, pp. 942-950
-
-
Curwen, V.1
-
15
-
-
0003552989
-
-
A model of evolutionary change in proteins, ed, National Biomedical Research Foundation, Silver Spring, ML, pp
-
Dayhoff,M.O. et al. (1978) A model of evolutionary change in proteins. In Dayhoff,M.O (ed.) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Spring, ML, pp. 345-352.
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
-
16
-
-
34548390530
-
Conrad: Gene prediction using conditional random fields
-
DeCaprio,D. et al. (2007) Conrad: Gene prediction using conditional random fields. Genome Res., 17, 1389-1398.
-
(2007)
Genome Res
, vol.17
, pp. 1389-1398
-
-
DeCaprio, D.1
-
17
-
-
1242320272
-
Local homology recognition and distance measures in linear time using compressed amino acid alphabets
-
Edgar,R.C. (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res. 32, 380-385.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 380-385
-
-
Edgar, R.C.1
-
18
-
-
0029830044
-
Gene recognition via spliced sequence alignment
-
Gelfand,M.S. et al. (1996) Gene recognition via spliced sequence alignment. Proc. Natl Acad. Sci. USA, 93, 9061-9066.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 9061-9066
-
-
Gelfand, M.S.1
-
19
-
-
33846659488
-
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
-
Gertz,E.M. et al. (2006) Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST. BMC Biol., 4, 41.
-
(2006)
BMC Biol
, vol.4
, pp. 41
-
-
Gertz, E.M.1
-
20
-
-
0031760236
-
Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes
-
Gotoh,O. (1998) Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Mol. Biol. Evol., 15, 1447-1459.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 1447-1459
-
-
Gotoh, O.1
-
21
-
-
0034129662
-
Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
-
Gotoh,O. (2000) Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics, 16, 190-202.
-
(2000)
Bioinformatics
, vol.16
, pp. 190-202
-
-
Gotoh, O.1
-
22
-
-
43349092271
-
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
-
Gotoh,O. (2008) A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res., 36, 2630-2638.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2630-2638
-
-
Gotoh, O.1
-
23
-
-
40449115745
-
CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction
-
Gross,S.S. et al. (2007) CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol., 8, R269.
-
(2007)
Genome Biol
, vol.8
-
-
Gross, S.S.1
-
24
-
-
0033782834
-
An assessment of gene prediction accuracy in large DNA sequences
-
Guigo,R. et al. (2000) An assessment of gene prediction accuracy in large DNA sequences. Genome Res., 10, 1631-1642.
-
(2000)
Genome Res
, vol.10
, pp. 1631-1642
-
-
Guigo, R.1
-
25
-
-
33748641351
-
-
EGASP: The human ENCODE genome annotation assessment project, Suppl. 1, S2 1-31
-
Guigo,R. et al. (2006) EGASP: The human ENCODE genome annotation assessment project. Genome Biol., 7 (Suppl. 1), S2 1-31.
-
(2006)
Genome Biol
, vol.7
-
-
Guigo, R.1
-
26
-
-
42949086676
-
Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
-
Haas,B.J. et al. (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol., 9, R7.
-
(2008)
Genome Biol
, vol.9
-
-
Haas, B.J.1
-
27
-
-
0028303880
-
An algorithm combining DNA and protein alignment
-
Hein,J. (1994) An algorithm combining DNA and protein alignment. J. Theor. Biol., 167, 169-174.
-
(1994)
J. Theor. Biol
, vol.167
, pp. 169-174
-
-
Hein, J.1
-
28
-
-
33747826336
-
GeneAlign: A coding exon prediction tool based on phylogenetical comparisons
-
Hsieh,S.J. et al. (2006) GeneAlign: A coding exon prediction tool based on phylogenetical comparisons. Nucleic Acids Res., 34, W280-W284.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Hsieh, S.J.1
-
29
-
-
0030446464
-
Methods for comparing a DNA sequence with a protein sequence
-
Huang,X. and Zhang,J. (1996) Methods for comparing a DNA sequence with a protein sequence. Comput. Appl. Biosci., 12, 497-506.
-
(1996)
Comput. Appl. Biosci
, vol.12
, pp. 497-506
-
-
Huang, X.1
Zhang, J.2
-
30
-
-
0031573382
-
A tool for analyzing and annotating genomic sequences
-
Huang,X. et al. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
-
(1997)
Genomics
, vol.46
, pp. 37-45
-
-
Huang, X.1
-
31
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
-
32
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones,D.T. et al. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
-
33
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
35
-
-
0036202921
-
PatternHunter: Faster and more sensitive homology search
-
Ma,B. et al. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
-
(2002)
Bioinformatics
, vol.18
, pp. 440-445
-
-
Ma, B.1
-
36
-
-
29244442741
-
Genome sequencing and analysis of Aspergillus oryzae
-
Machida,M. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature, 438, 1157-1161.
-
(2005)
Nature
, vol.438
, pp. 1157-1161
-
-
Machida, M.1
-
37
-
-
1342263801
-
Gene structure conservation aids similarity based gene prediction
-
Meyer,I.M. and Durbin,R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res., 32, 776-783.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 776-783
-
-
Meyer, I.M.1
Durbin, R.2
-
38
-
-
0024236865
-
Sequence comparison with concave weighting functions
-
Miller,W. and Myers,E.W. (1988) Sequence comparison with concave weighting functions. Bull. Math. Biol., 50, 97-120.
-
(1988)
Bull. Math. Biol
, vol.50
, pp. 97-120
-
-
Miller, W.1
Myers, E.W.2
-
39
-
-
0001338954
-
Simplified amino acid alphabets for protein fold recognition and implications for folding
-
Murphy,L.R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng. 13, 149-152.
-
(2000)
Protein Eng
, vol.13
, pp. 149-152
-
-
Murphy, L.R.1
-
40
-
-
14044252770
-
Patterns of intron gain and loss in fungi
-
Nielsen,C.B. et al. (2004) Patterns of intron gain and loss in fungi. PLoS Biol., 2, e422.
-
(2004)
PLoS Biol
, vol.2
-
-
Nielsen, C.B.1
-
41
-
-
0041695455
-
Five hundred sixty-five triples of chicken, human, and mouse candidate orthologs
-
Ouyang,M, et al. (2003) Five hundred sixty-five triples of chicken, human, and mouse candidate orthologs. J. Mol. Evol., 57, 271-281.
-
(2003)
J. Mol. Evol
, vol.57
, pp. 271-281
-
-
Ouyang, M.1
-
42
-
-
0033381623
-
Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
-
Pavy,N. et al. (1999) Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
-
(1999)
Bioinformatics
, vol.15
, pp. 887-899
-
-
Pavy, N.1
-
43
-
-
0031573415
-
Comparison of DNA sequences with protein sequences
-
Pearson,W.R. et al. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
-
(1997)
Genomics
, vol.46
, pp. 24-36
-
-
Pearson, W.R.1
-
44
-
-
0022609080
-
Algorithms for the search of amino acid patterns in nucleic acid sequences
-
Peltola,H. et al. (1986) Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucleic Acids Res., 14, 99-107.
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 99-107
-
-
Peltola, H.1
-
45
-
-
0035002807
-
Evaluation of gene-finding programs on mammalian sequences
-
Rogic,S. et al. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
-
(2001)
Genome Res
, vol.11
, pp. 817-832
-
-
Rogic, S.1
-
46
-
-
0030869663
-
A method for identifying splice sites and translational start sites in eukaryotic mRNA
-
Salzberg,S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci. 13, 365-376.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 365-376
-
-
Salzberg, S.L.1
-
47
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
48
-
-
3242889577
-
AUGUSTUS: A web server for gene finding in eukaryotes
-
Stanke,M. et al. (2004) AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Res., 32, W309-W312.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Stanke, M.1
-
49
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative
-
The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
50
-
-
0032509302
-
-
The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
-
The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
-
-
-
-
51
-
-
0034646570
-
Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring
-
Usuka,J. and Brendel,V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 1075-1085
-
-
Usuka, J.1
Brendel, V.2
-
52
-
-
33646493012
-
SPA: A probabilistic algorithm for spliced alignment
-
van Nimwegen,E. et al. (2006) SPA: A probabilistic algorithm for spliced alignment. PLoS Genet., 2, e24.
-
(2006)
PLoS Genet
, vol.2
-
-
van Nimwegen, E.1
-
53
-
-
33644876253
-
Database resources of the national center for biotechnology information
-
Wheeler,D.L. et al. (2006) Database resources of the national center for biotechnology information. Nucleic Acids Res., 34 D173-D180.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wheeler, D.L.1
-
54
-
-
18744383071
-
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
-
Wu,T.D. and Watanabe,C.K. (2005) GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
55
-
-
0035002015
-
Computational inference of homologous gene structures in the human genome
-
Yeh,R.F. et al. (2001) Computational inference of homologous gene structures in the human genome. Genome Res., 11, 803-816.
-
(2001)
Genome Res
, vol.11
, pp. 803-816
-
-
Yeh, R.F.1
-
56
-
-
0027377256
-
a weight assay method for splicing signal analysis
-
Zhang,M.Q. and Marr,T.G. (1993) a weight assay method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
-
(1993)
Comput. Appl. Biosci
, vol.9
, pp. 499-509
-
-
Zhang, M.Q.1
Marr, T.G.2
-
57
-
-
0141838143
-
Spliceosomal introns: New insights into their evolution
-
Zhaxybayeva,O. and Gogarten,J.P. (2003) Spliceosomal introns: New insights into their evolution. Curr. Biol., 13, R764-R766.
-
(2003)
Curr. Biol
, vol.13
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
|