-
1
-
-
0027059264
-
Assessment of protein coding measures
-
Fickett J.W., Tung C.S. Assessment of protein coding measures. Nucleic Acids Res. 20:1992;6441-6450.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 6441-6450
-
-
Fickett, J.W.1
Tung, C.S.2
-
2
-
-
0030768930
-
Computational methods for the identification of genes in vertebrate genomic sequences
-
Claverie J.M. Computational methods for the identification of genes in vertebrate genomic sequences. Hum Mol Genet. 6:1997;1735-1744.
-
(1997)
Hum Mol Genet
, vol.6
, pp. 1735-1744
-
-
Claverie, J.M.1
-
3
-
-
0030787474
-
Computational gene identification
-
Guigó R. Computational gene identification. J Mol Med. 75:1997;389-393.
-
(1997)
J Mol Med
, vol.75
, pp. 389-393
-
-
Guigó, R.1
-
5
-
-
11544300316
-
Computational genefinding
-
Haussler D. Computational genefinding. Trends Biochem Sci. suppl:1998;12-15.
-
(1998)
Trends Biochem Sci
, pp. 12-15
-
-
Haussler, D.1
-
6
-
-
0033616509
-
Gene identification in bacterial and organellar genomes using GeneScan
-
Ramakrishna R., Srinivasan R. Gene identification in bacterial and organellar genomes using GeneScan. Comput Chem. 23:1999;165-174.
-
(1999)
Comput Chem
, vol.23
, pp. 165-174
-
-
Ramakrishna, R.1
Srinivasan, R.2
-
7
-
-
0033166634
-
Interpolated Markov models for eukaryotic gene-finding
-
Salzberg S.L., Pertea M., Delcher A.L., Gardner M.J., Tettelin H. Interpolated Markov models for eukaryotic gene-finding. Genomics. 59:1999;24-31.
-
(1999)
Genomics
, vol.59
, pp. 24-31
-
-
Salzberg, S.L.1
Pertea, M.2
Delcher, A.L.3
Gardner, M.J.4
Tettelin, H.5
-
8
-
-
0034098729
-
Genome annotation assessment in Drosophila melanogaster
-
The April 2000 issue of Genome Research (see Note added in proof) includes both descriptions and evaluations of the Genome Annotation Assessment Project
-
Reese M.G., Hartzell G., Harris N.L., Ohler U., Lewis S.E. Genome annotation assessment in Drosophila melanogaster. Genome Res. 10:2000;483-501. The April 2000 issue of Genome Research (see Note added in proof) includes both descriptions and evaluations of the Genome Annotation Assessment Project.
-
(2000)
Genome Res
, vol.10
, pp. 483-501
-
-
Reese, M.G.1
Hartzell, G.2
Harris, N.L.3
Ohler, U.4
Lewis, S.E.5
-
9
-
-
0032857480
-
An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster. The Adh region
-
Ashburner M., Misra S., Roote J., Lewis S.E., Blazej R., Davis T., Doyle C., Galle R., George R., Harris N.et al. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster. The Adh region. Genetics. 153:1999;179-219.
-
(1999)
Genetics
, vol.153
, pp. 179-219
-
-
Ashburner, M.1
Misra, S.2
Roote, J.3
Lewis, S.E.4
Blazej, R.5
Davis, T.6
Doyle, C.7
Galle, R.8
George, R.9
Harris, N.10
-
10
-
-
0030585734
-
Evaluation of gene structure prediction programs
-
Burset M., Guigó R. Evaluation of gene structure prediction programs. Genomics. 34:1996;353-367.
-
(1996)
Genomics
, vol.34
, pp. 353-367
-
-
Burset, M.1
Guigó, R.2
-
11
-
-
0033534799
-
Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences
-
Rogozin I.B., D'Angelo D., Milanesi L. Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. Gene. 226:1999;129-137.
-
(1999)
Gene
, vol.226
, pp. 129-137
-
-
Rogozin, I.B.1
D'Angelo, D.2
Milanesi, L.3
-
12
-
-
0032822836
-
GeneBuilder: Interactive in silico prediction of gene structure
-
Milanesi L., D'Angelo D., Rogozin I.B. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 15:1999;612-621.
-
(1999)
Bioinformatics
, vol.15
, pp. 612-621
-
-
Milanesi, L.1
D'Angelo, D.2
Rogozin, I.B.3
-
13
-
-
0028685587
-
Optimally parsing a sequence into different classes based on multiple types of evidence
-
Stormo G.D., Haussler D. Optimally parsing a sequence into different classes based on multiple types of evidence. Ismb. 2:1994;369-375.
-
(1994)
Ismb
, vol.2
, pp. 369-375
-
-
Stormo, G.D.1
Haussler, D.2
-
14
-
-
0030333286
-
A generalized hidden Markov model for the recognition of human genes in DNA
-
Kulp D., Haussler D., Reese M.G., Eeckman F.H. A generalized hidden Markov model for the recognition of human genes in DNA. Ismb. 4:1996;134-142.
-
(1996)
Ismb
, vol.4
, pp. 134-142
-
-
Kulp, D.1
Haussler, D.2
Reese, M.G.3
Eeckman, F.H.4
-
16
-
-
0033025047
-
Promoter2.0: For the recognition of PolII promoter sequences
-
•], describes statistically clean approaches to the hard problem of identifying promoters in eukaryotic genome sequences
-
•], describes statistically clean approaches to the hard problem of identifying promoters in eukaryotic genome sequences.
-
(1999)
Bioinformatics
, vol.15
, pp. 356-361
-
-
Knudsen, S.1
-
18
-
-
0033064714
-
Starts of bacterial genes: Estimating the reliability of computer predictions
-
Frishman D., Mironov A., Gelfand M. Starts of bacterial genes: estimating the reliability of computer predictions. Gene. 234:1999;257-265.
-
(1999)
Gene
, vol.234
, pp. 257-265
-
-
Frishman, D.1
Mironov, A.2
Gelfand, M.3
-
19
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
This paper presents a novel method for detecting repeat elements in DNA in a rigorous statistical framework
-
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:1999;573-580. This paper presents a novel method for detecting repeat elements in DNA in a rigorous statistical framework.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
20
-
-
0033066718
-
REPuter: Fast computation of maximal repeats in complete genomes
-
Kurtz S., Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics. 15:1999;426-427.
-
(1999)
Bioinformatics
, vol.15
, pp. 426-427
-
-
Kurtz, S.1
Schleiermacher, C.2
-
21
-
-
0032952825
-
New features of the Blocks Database servers
-
The BLOCKS database is a tremendous resource for identifying protein motifs. It was used extensively in the annotation of the Drosophila genome (see Note added in proof)
-
Henikoff J.G., Henikoff S., Pietrokovski S. New features of the Blocks Database servers. Nucleic Acids Res. 27:1999;226-228. The BLOCKS database is a tremendous resource for identifying protein motifs. It was used extensively in the annotation of the Drosophila genome (see Note added in proof).
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 226-228
-
-
Henikoff, J.G.1
Henikoff, S.2
Pietrokovski, S.3
-
22
-
-
0032776495
-
Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
-
Henikoff S., Henikoff J.G., Pietrokovski S. Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics. 15:1999;471-479.
-
(1999)
Bioinformatics
, vol.15
, pp. 471-479
-
-
Henikoff, S.1
Henikoff, J.G.2
Pietrokovski, S.3
-
23
-
-
0031732094
-
A computer program for aligning a cDNA sequence with a genomic DNA sequence
-
Florea L., Hartzell G., Zhang Z., Rubin G.M., Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8:1998;967-974.
-
(1998)
Genome Res
, vol.8
, pp. 967-974
-
-
Florea, L.1
Hartzell, G.2
Zhang, Z.3
Rubin, G.M.4
Miller, W.5
-
24
-
-
85031639882
-
-
ACEMBLY on World Wide Web URL
-
ACEMBLY on World Wide Web URL: http://alpha.crbm.cnrs-mop.fr/acembly/ .
-
-
-
-
25
-
-
0032944238
-
The PROSITE database, its status in 1999
-
Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:1999;215-219.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
26
-
-
0033957801
-
PRINTS-S: The database formerly known as PRINTS
-
Attwood T.K., Croning M.D., Flower D.R., Lewis A.P., Mabey J.E., Scordis P., Selley J.N., Wright W. PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res. 28:2000;225-227.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 225-227
-
-
Attwood, T.K.1
Croning, M.D.2
Flower, D.R.3
Lewis, A.P.4
Mabey, J.E.5
Scordis, P.6
Selley, J.N.7
Wright, W.8
-
27
-
-
0033976458
-
The Pfam protein families database
-
Bateman A., Birney E., Durbin R., Eddy S.R., Howe K.L., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 28:2000;263-266.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 263-266
-
-
Bateman, A.1
Birney, E.2
Durbin, R.3
Eddy, S.R.4
Howe, K.L.5
Sonnhammer, E.L.6
-
28
-
-
0032952229
-
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
-
Bateman A., Birney E., Durbin R., Eddy S.R., Finn R.D., Sonnhammer E.L. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27:1999;260-262.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 260-262
-
-
Bateman, A.1
Birney, E.2
Durbin, R.3
Eddy, S.R.4
Finn, R.D.5
Sonnhammer, E.L.6
-
29
-
-
0033957841
-
ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
-
Corpet F., Servant F., Gouzy J., Kahn D. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28:2000;267-269.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 267-269
-
-
Corpet, F.1
Servant, F.2
Gouzy, J.3
Kahn, D.4
-
30
-
-
0344417851
-
A novel method for automatic functional annotation of proteins
-
Semiautomated protein function assignment using InterPro is the best resource for comprehensively studying newly discovered genes
-
Fleischmann W., Moller S., Gateau A., Apweiler R. A novel method for automatic functional annotation of proteins. Bioinformatics. 15:1999;228-233. Semiautomated protein function assignment using InterPro is the best resource for comprehensively studying newly discovered genes.
-
(1999)
Bioinformatics
, vol.15
, pp. 228-233
-
-
Fleischmann, W.1
Moller, S.2
Gateau, A.3
Apweiler, R.4
-
31
-
-
85031640451
-
-
Wise2 on World Wide Web URL
-
Wise2 on World Wide Web URL: http://www.sanger.ac.uk/Software/Wise2/ .
-
-
-
-
32
-
-
0032884653
-
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
-
Jareborg N., Birney E., Durbin R. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res. 9:1999;815-824.
-
(1999)
Genome Res
, vol.9
, pp. 815-824
-
-
Jareborg, N.1
Birney, E.2
Durbin, R.3
-
33
-
-
0032787618
-
A comparison of sequence and structure protein domain families as a basis for structural genomics
-
Elofsson A., Sonnhammer E.L. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics. 15:1999;480-500.
-
(1999)
Bioinformatics
, vol.15
, pp. 480-500
-
-
Elofsson, A.1
Sonnhammer, E.L.2
-
34
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Studying protein domains in complete genomes gives many clues about the evolution and function of genes
-
Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 402:1999;83-86. Studying protein domains in complete genomes gives many clues about the evolution and function of genes.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
35
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
36
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Studying protein domains in complete genomes gives many clues about the evolution and function of genes
-
Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 402:1999;86-90. Studying protein domains in complete genomes gives many clues about the evolution and function of genes.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
37
-
-
0033034745
-
Automated genome sequence analysis and annotation
-
Andrade M.A., Brown N.P., Leroy C., Hoersch S., de Daruvar A., Reich C., Franchini A., Tamames J., Valencia A., Ouzounis C.et al. Automated genome sequence analysis and annotation. Bioinformatics. 15:1999;391-412.
-
(1999)
Bioinformatics
, vol.15
, pp. 391-412
-
-
Andrade, M.A.1
Brown, N.P.2
Leroy, C.3
Hoersch, S.4
De Daruvar, A.5
Reich, C.6
Franchini, A.7
Tamames, J.8
Valencia, A.9
Ouzounis, C.10
-
38
-
-
0032890635
-
The Genome Channel: A browser to a uniform first-pass annotation of genomic DNA
-
Mural R.J., Parang M., Shah M., Snoddy J., Uberbacher E.C. The Genome Channel: a browser to a uniform first-pass annotation of genomic DNA. Trends Genet. 15:1999;38-39.
-
(1999)
Trends Genet
, vol.15
, pp. 38-39
-
-
Mural, R.J.1
Parang, M.2
Shah, M.3
Snoddy, J.4
Uberbacher, E.C.5
-
39
-
-
85031645310
-
-
ensEMBL on World Wide Web URL: A landmark in the automatic annotation of eukaryotic sequences on a very large scale
-
ensEMBL on World Wide Web URL: http://www.ensemble.org/ . A landmark in the automatic annotation of eukaryotic sequences on a very large scale.
-
-
-
-
40
-
-
79960655760
-
The DNA sequence of human chromosome 22
-
Dunham I., Shimizu N., Roe B.A., Chissoe S., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J.et al. The DNA sequence of human chromosome 22. Nature. 402:1999;489-495.
-
(1999)
Nature
, vol.402
, pp. 489-495
-
-
Dunham, I.1
Shimizu, N.2
Roe, B.A.3
Chissoe, S.4
Hunt, A.R.5
Collins, J.E.6
Bruskiewich, R.7
Beare, D.M.8
Clamp, M.9
Smink, L.J.10
-
41
-
-
85031647380
-
-
GeneScene on World Wide Web URL
-
GeneScene on World Wide Web URL: http://www.fruitfly.org/annot/genescene-launch-static.html .
-
-
-
-
42
-
-
85031639517
-
-
Jalview on World Wide Web URL
-
Jalview on World Wide Web URL: http://www.ebi.ac.uk/~michele/jalview/contents.html .
-
-
-
-
43
-
-
0029173791
-
Identification of human gene structure using linear discriminant functions and dynamic programming
-
Solovyev V.V., Salamov A.A., Lawrence C.B. Identification of human gene structure using linear discriminant functions and dynamic programming. Ismb. 3:1995;367-375.
-
(1995)
Ismb
, vol.3
, pp. 367-375
-
-
Solovyev, V.V.1
Salamov, A.A.2
Lawrence, C.B.3
-
44
-
-
0031298797
-
Computational gene identification: An open problem
-
Guigo R. Computational gene identification: an open problem. Comput Chem. 21:1997;215-222.
-
(1997)
Comput Chem
, vol.21
, pp. 215-222
-
-
Guigo, R.1
-
45
-
-
0032456609
-
Assembling genes from predicted exons in linear time with dynamic programming
-
Guigo R. Assembling genes from predicted exons in linear time with dynamic programming. J Comput Biol. 5:1998;681-702.
-
(1998)
J Comput Biol
, vol.5
, pp. 681-702
-
-
Guigo, R.1
-
47
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 268:1997;78-94.
-
(1997)
J Mol Biol
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
48
-
-
0030623944
-
Two methods for improving performance of an HMM and their application for gene-finding
-
Krogh A. Two methods for improving performance of an HMM and their application for gene-finding. Ismb. 5:1997;179-186.
-
(1997)
Ismb
, vol.5
, pp. 179-186
-
-
Krogh, A.1
-
49
-
-
0033214628
-
Heuristic approach to deriving models for gene-finding
-
Besemer J., Borodovsky M. Heuristic approach to deriving models for gene-finding. Nucleic Acids Res. 27:1999;3911-3920.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3911-3920
-
-
Besemer, J.1
Borodovsky, M.2
-
50
-
-
0026351408
-
Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach
-
Uberbacher E.C., Mural R.J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl Acad Sci USA. 88:1991;11 261-11 265.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 11261-11265
-
-
Uberbacher, E.C.1
Mural, R.J.2
-
51
-
-
0030628597
-
Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison
-
Birney E., Durbin R. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Ismb. 5:1997;56-64.
-
(1997)
Ismb
, vol.5
, pp. 56-64
-
-
Birney, E.1
Durbin, R.2
-
52
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.et al. The genome sequence of Drosophila melanogaster. Science. 287:2000;2185-2195.
-
(2000)
Science
, vol.287
, pp. 2185-2195
-
-
Adams, M.D.1
Celniker, S.E.2
Holt, R.A.3
Evans, C.A.4
Gocayne, J.D.5
Amanatides, P.G.6
Scherer, S.E.7
Li, P.W.8
Hoskins, R.A.9
Galle, R.F.10
-
53
-
-
0034708444
-
Comparative genomics of the eukaryotes
-
Rubin G.M., Yandell M.D., Wortman J.R., Gabor Miklos G.L., Nelson C.R., Hariharan I.K., Fortini M.E., Li P.W., Apweiler R., Fleischmann W.et al. Comparative genomics of the eukaryotes. Science. 287:2000;2204-2215.
-
(2000)
Science
, vol.287
, pp. 2204-2215
-
-
Rubin, G.M.1
Yandell, M.D.2
Wortman, J.R.3
Gabor Miklos, G.L.4
Nelson, C.R.5
Hariharan, I.K.6
Fortini, M.E.7
Li, P.W.8
Apweiler, R.9
Fleischmann, W.10
|