-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, 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
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
2
-
-
12344295510
-
A probabilistic measure for alignment-free sequence comparison
-
Pham TD, Zuegg J, (2004) A probabilistic measure for alignment-free sequence comparison. Bioinformatics 20: 3455-3461.
-
(2004)
Bioinformatics
, vol.20
, pp. 3455-3461
-
-
Pham, T.D.1
Zuegg, J.2
-
3
-
-
33750358065
-
Spectral distortion measures for biological sequence comparisons and database searching
-
Pham TD, (2007) Spectral distortion measures for biological sequence comparisons and database searching. Pattern Recog 40: 516-529.
-
(2007)
Pattern Recog
, vol.40
, pp. 516-529
-
-
Pham, T.D.1
-
4
-
-
48249137399
-
Similarity Queries for Temporal Toxicogenomic Expression Profiles
-
Smith AA, Vollrath A, Bradfield CA, Craven M, (2008) Similarity Queries for Temporal Toxicogenomic Expression Profiles. PLoS Comput Biol 4 (7): e1000116.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.7
-
-
Smith, A.A.1
Vollrath, A.2
Bradfield, C.A.3
Craven, M.4
-
5
-
-
53749097779
-
Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison
-
Dai Q, Yang YC, Wang TM, (2008) Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 24: 2296-2302.
-
(2008)
Bioinformatics
, vol.24
, pp. 2296-2302
-
-
Dai, Q.1
Yang, Y.C.2
Wang, T.M.3
-
6
-
-
34547844142
-
A statistical method for alignment-free comparison of regulatory sequences
-
Kantorovitz MR, Robinson GE, Sinha S, (2007) A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23: i249-i255.
-
(2007)
Bioinformatics
, vol.23
-
-
Kantorovitz, M.R.1
Robinson, G.E.2
Sinha, S.3
-
7
-
-
1342309208
-
Metrics for comparing regulatory sequences on the basis of pattern counts
-
Van Helden J, (2004) Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20: 399-406.
-
(2004)
Bioinformatics
, vol.20
, pp. 399-406
-
-
Van Helden, J.1
-
8
-
-
36949006682
-
MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules
-
Sinha S, He X, (2007) MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PLoS Comput Biol 3 (11): e216.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.11
-
-
Sinha, S.1
He, X.2
-
9
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance and like-lihood methods
-
Felsenstein J, (1996) Inferring phylogenies from protein sequences by parsimony, distance and like-lihood methods. Meth Enzymol 266: 418-427.
-
(1996)
Meth Enzymol
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
10
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
11
-
-
3242810318
-
MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment
-
Kumar S, Tamura K, Nei M, (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefing Bioinform 5: 150-163.
-
(2004)
Briefing Bioinform
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
12
-
-
0035102453
-
An information-based sequence distance and its application to whole mitochondrial genome phylogeny
-
Li M, Badger JH, Chen X, Kwong S, Kearney P, et al. (2001) An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17: 149-154.
-
(2001)
Bioinformatics
, vol.17
, pp. 149-154
-
-
Li, M.1
Badger, J.H.2
Chen, X.3
Kwong, S.4
Kearney, P.5
-
13
-
-
0242643741
-
A new sequence distance measure for phylogenetic tree construction
-
Otu HH, Sayood K, (2003) A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19: 2122-2130.
-
(2003)
Bioinformatics
, vol.19
, pp. 2122-2130
-
-
Otu, H.H.1
Sayood, K.2
-
14
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
15
-
-
33846491679
-
A phylogenomic study of human, dog, and mouse
-
Cannarozzi G, Schneider A, Gonnet G, (2007) A phylogenomic study of human, dog, and mouse. PLoS Comput Biol 3 (1): e2.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.1
-
-
Cannarozzi, G.1
Schneider, A.2
Gonnet, G.3
-
16
-
-
33846537828
-
Using phylogeny to improve genome-wide distant homology recognition
-
Abeln S, Teubner C, Deane CM, (2007) Using phylogeny to improve genome-wide distant homology recognition. PLoS Comput Biol 3 (1): e3.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.1
-
-
Abeln, S.1
Teubner, C.2
Deane, C.M.3
-
17
-
-
52949150097
-
Probabilistic Phylogenetic Inference with Insertions and Deletions
-
Rivas E, Eddy SR, (2008) Probabilistic Phylogenetic Inference with Insertions and Deletions. PLoS Comput Biol 4 (9): e1000172.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.9
-
-
Rivas, E.1
Eddy, S.R.2
-
18
-
-
59149089414
-
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
-
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A, (2009) Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. PLoS Comput Biol 5 (1): e1000267.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.1
-
-
Engelen, S.1
Trojan, L.A.2
Sacquin-Mora, S.3
Lavery, R.4
Carbone, A.5
-
19
-
-
0034945722
-
Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of Panax vietnamensis and five related species
-
Komatsu K, Zhu S, Fushimi H, Qui TK, Cai S, et al. (2001) Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of Panax vietnamensis and five related species. Planta Med 67: 461-465.
-
(2001)
Planta Med
, vol.67
, pp. 461-465
-
-
Komatsu, K.1
Zhu, S.2
Fushimi, H.3
Qui, T.K.4
Cai, S.5
-
20
-
-
4444270864
-
Cluster-C: an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques
-
Mohseni-Zadeh S, Brezellec P, Risler JL, (2004) Cluster-C: an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques. Comput Biol Chem 28: 211-218.
-
(2004)
Comput Biol Chem
, vol.28
, pp. 211-218
-
-
Mohseni-Zadeh, S.1
Brezellec, P.2
Risler, J.L.3
-
21
-
-
0346652457
-
ProClust: improved clustering of protein sequences with an extended graph-based approach
-
Pipenbacher P, Schliep A, Schneckener S, Schonhuth A, Schomburg D, et al. (2002) ProClust: improved clustering of protein sequences with an extended graph-based approach. Bioinformatics 18: S182-S191.
-
(2002)
Bioinformatics
, vol.18
-
-
Pipenbacher, P.1
Schliep, A.2
Schneckener, S.3
Schonhuth, A.4
Schomburg, D.5
-
22
-
-
33751415854
-
3D Complex: A structural classification of protein complexes
-
Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA, (2006) 3D Complex: A structural classification of protein complexes. PLoS Comput Biol 2 (11): e155.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.11
-
-
Levy, E.D.1
Pereira-Leal, J.B.2
Chothia, C.3
Teichmann, S.A.4
-
24
-
-
0003512471
-
-
Chapman and Hall/CRC, Boca Raton, FL
-
Waterman MS, (1995) Introduction to Computational Biology: Maps, Sequences, and Genomes: Interdisciplinary Statistics, Chapman and Hall/CRC, Boca Raton, FL.
-
(1995)
Introduction to Computational Biology: Maps, Sequences, and Genomes: Interdisciplinary Statistics
-
-
Waterman, M.S.1
-
26
-
-
0037342499
-
Alignment-free sequence comparison-a review
-
Vinga S, Almeida J, (2003) Alignment-free sequence comparison-a review. Bioinformatics 19: 513-523.
-
(2003)
Bioinformatics
, vol.19
, pp. 513-523
-
-
Vinga, S.1
Almeida, J.2
-
27
-
-
0022743812
-
Ameasure of the similarity of sets of sequences not requiring sequence alignment
-
Blaisdell BE, (1986) Ameasure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci USA 83: 5155-5159.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 5155-5159
-
-
Blaisdell, B.E.1
-
28
-
-
0031437248
-
A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words
-
Wu TJ, Burke JP, Davison DB, (1997) A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics 53: 1431-1439.
-
(1997)
Biometrics
, vol.53
, pp. 1431-1439
-
-
Wu, T.J.1
Burke, J.P.2
Davison, D.B.3
-
29
-
-
0035013276
-
Statistical measures of DNA dissimilarity under Markov chain models of base composition
-
Wu TJ, Hsieh YC, Li LA, (2001) Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics 57: 441-448.
-
(2001)
Biometrics
, vol.57
, pp. 441-448
-
-
Wu, T.J.1
Hsieh, Y.C.2
Li, L.A.3
-
30
-
-
33646005790
-
The average common substring approach to phylogenomic reconstruction
-
Ulitsky I, Burstein D, Tuller T, Chor B, (2006) The average common substring approach to phylogenomic reconstruction. J Comput Biol 13: 336-350.
-
(2006)
J Comput Biol
, vol.13
, pp. 336-350
-
-
Ulitsky, I.1
Burstein, D.2
Tuller, T.3
Chor, B.4
-
31
-
-
0036166508
-
Integrated gene and species phylogenies from unaligned whole genome protein sequences
-
Stuart GW, Moffett K, Baker S, (2002) Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics 18: 100-108.
-
(2002)
Bioinformatics
, vol.18
, pp. 100-108
-
-
Stuart, G.W.1
Moffett, K.2
Baker, S.3
-
32
-
-
0023450024
-
Statistical method for predicting protein coding regions in nucleic acid sequences
-
Fichant G, Gautier C, (1987) Statistical method for predicting protein coding regions in nucleic acid sequences. Comput Appl Biosci 3: 287-295.
-
(1987)
Comput Appl Biosci
, vol.3
, pp. 287-295
-
-
Fichant, G.1
Gautier, C.2
-
33
-
-
3242889314
-
Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance
-
Hao B, Qi J, (2004) Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J Bioinform Comput Biol 2: 1-19.
-
(2004)
J Bioinform Comput Biol
, vol.2
, pp. 1-19
-
-
Hao, B.1
Qi, J.2
-
34
-
-
33748796945
-
Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method
-
Wu X, Wan X, Wu G, Xu D, Lin G, (2006) Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. Int J Bioinform Res Appl 2: 219-248.
-
(2006)
Int J Bioinform Res Appl
, vol.2
, pp. 219-248
-
-
Wu, X.1
Wan, X.2
Wu, G.3
Xu, D.4
Lin, G.5
-
35
-
-
58149496557
-
Fast algorithms for computing sequence distances by exhaustive substring composition
-
Apostolico A, Denas O, (2008) Fast algorithms for computing sequence distances by exhaustive substring composition. Algorithms Mol Biol 3: 13.
-
(2008)
Algorithms Mol Biol
, vol.3
, pp. 13
-
-
Apostolico, A.1
Denas, O.2
-
36
-
-
47249127227
-
An improved string composition method for sequence comparison
-
Lu GQ, Zhang SP, Fang X, (2008) An improved string composition method for sequence comparison. BMC Bioinformatics 9 (Suppl 6): S15.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 6
-
-
Lu, G.Q.1
Zhang, S.P.2
Fang, X.3
-
37
-
-
0042831182
-
Evolutionarily conserved pattern of gene segment usage within the mammalian TCRbeta locus
-
Livak F, (2003) Evolutionarily conserved pattern of gene segment usage within the mammalian TCRbeta locus. Immunogenetics 55: 307-314.
-
(2003)
Immunogenetics
, vol.55
, pp. 307-314
-
-
Livak, F.1
-
38
-
-
33846698069
-
Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression
-
Dixon RJ, Eperon IC, Samani NJ, (2007) Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. Bioinformatics 23: 150-155.
-
(2007)
Bioinformatics
, vol.23
, pp. 150-155
-
-
Dixon, R.J.1
Eperon, I.C.2
Samani, N.J.3
-
39
-
-
0030839806
-
An E±cient Statistic to Detect Over-and Under-Represented Words in DNA Sequences
-
Schbath S, (1997) An E±cient Statistic to Detect Over-and Under-Represented Words in DNA Sequences. J Comp Biol 4 (2): 189-192.
-
(1997)
J Comp Biol
, vol.4
, Issue.2
, pp. 189-192
-
-
Schbath, S.1
-
40
-
-
0034125366
-
Probabilistic and statistical properties of words: an overview
-
Reinert G, Schbath S, Waterman MS, (2000) Probabilistic and statistical properties of words: an overview. J Comput Biol 7: 1-46.
-
(2000)
J Comput Biol
, vol.7
, pp. 1-46
-
-
Reinert, G.1
Schbath, S.2
Waterman, M.S.3
-
41
-
-
0033238297
-
Exact distribution of word occurrences in a random sequence of letters
-
Robin S, Daudin JJ, (1999) Exact distribution of word occurrences in a random sequence of letters. J Appl Prob 36: 179-193.
-
(1999)
J Appl Prob
, vol.36
, pp. 179-193
-
-
Robin, S.1
Daudin, J.J.2
-
42
-
-
27944497396
-
Sensitivity and convergence of uniformly ergodic Markov chains
-
Mitrophanov AY, (2005) Sensitivity and convergence of uniformly ergodic Markov chains. J Appl Prob 42: 1003-1014.
-
(2005)
J Appl Prob
, vol.42
, pp. 1003-1014
-
-
Mitrophanov, A.Y.1
-
45
-
-
0031191630
-
The use of the area under the ROC curve in the evaluation of machine learning algorithms
-
Bradley AP, (1997) The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recog 30: 1145-1159.
-
(1997)
Pattern Recog
, vol.30
, pp. 1145-1159
-
-
Bradley, A.P.1
-
46
-
-
0345983651
-
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison
-
Green RE, Brenner SE, (2002) Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc IEEE 90: 1834-1847.
-
(2002)
Proc IEEE
, vol.90
, pp. 1834-1847
-
-
Green, R.E.1
Brenner, S.E.2
-
48
-
-
32144456548
-
REDfly: a Regulatory Element Database for Drosophila
-
Gallo SM, Li L, Hu Z, Halfon MS, (2006) REDfly: a Regulatory Element Database for Drosophila. Bioinformatics 22: 381-383.
-
(2006)
Bioinformatics
, vol.22
, pp. 381-383
-
-
Gallo, S.M.1
Li, L.2
Hu, Z.3
Halfon, M.S.4
-
49
-
-
0037195172
-
Distributional regimes for the number of k-word matches between two random sequences
-
Lippert RA, Huang HY, Waterman MS, (2002) Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci USA 99: 13980C13989.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
-
-
Lippert, R.A.1
Huang, H.Y.2
Waterman, M.S.3
-
51
-
-
84929026405
-
Classification of short human exons and introns based on statistical features
-
Wu YH, Liew AWC, Yan H, Yang MS, (2003) Classification of short human exons and introns based on statistical features. PHYSICAL REVIEW E 67 (6): 061916.
-
(2003)
PHYSICAL REVIEW E
, vol.67
, Issue.6
, pp. 061916
-
-
Wu, Y.H.1
Liew, A.W.C.2
Yan, H.3
Yang, M.S.4
-
52
-
-
39149145162
-
Segmentation of short human exons based on spectral features of double curves
-
Jiang R, Yan H, (2008) Segmentation of short human exons based on spectral features of double curves. IJDMB 2 (1): 15-35.
-
(2008)
IJDMB
, vol.2
, Issue.1
, pp. 15-35
-
-
Jiang, R.1
Yan, H.2
-
53
-
-
43049175149
-
Studies of spectral properties of short genes using the wavelet subspace Hilbert Huang transform(WSHHT)[J]
-
Jiang R, Yan H, (2008) Studies of spectral properties of short genes using the wavelet subspace Hilbert Huang transform(WSHHT)[J]. Physica A 387: 4223-4247.
-
(2008)
Physica A
, vol.387
, pp. 4223-4247
-
-
Jiang, R.1
Yan, H.2
-
54
-
-
31144477556
-
Phylogenetic analysis of global hepatitis E virus sequences: genetic diversity, subtypes and zoonosis
-
Lu L, Li C, Hagedorn CH, (2006) Phylogenetic analysis of global hepatitis E virus sequences: genetic diversity, subtypes and zoonosis. Rev Med Virol 16: 5-36.
-
(2006)
Rev Med Virol
, vol.16
, pp. 5-36
-
-
Lu, L.1
Li, C.2
Hagedorn, C.H.3
-
55
-
-
45549086279
-
Molecular characterization and phylogenetic analysis of the complete genome of a hepatitis E virus from European swine
-
Xia HY, Liu LH, Linde AM, Belak S, Norder H, et al. (2008) Molecular characterization and phylogenetic analysis of the complete genome of a hepatitis E virus from European swine. Virus Genes 37: 39C48.
-
(2008)
Virus Genes
, vol.37
-
-
Xia, H.Y.1
Liu, L.H.2
Linde, A.M.3
Belak, S.4
Norder, H.5
-
56
-
-
60649116779
-
Phylogeny, classification and evolutionary insights into pestiviruses
-
Liu L, Xia H, Wahlberg N, Belok S, Baule C, (2009) Phylogeny, classification and evolutionary insights into pestiviruses. Virology 385: 351C357.
-
(2009)
Virology
, vol.385
-
-
Liu, L.1
Xia, H.2
Wahlberg, N.3
Belok, S.4
Baule, C.5
-
57
-
-
77549084603
-
Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing
-
Olvera A, Busquets N, Cortey M, de Deus N, Ganges L, et al. (2010) Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing. Vet J 184 (2): 130-137.
-
(2010)
Vet J
, vol.184
, Issue.2
, pp. 130-137
-
-
Olvera, A.1
Busquets, N.2
Cortey, M.3
de Deus, N.4
Ganges, L.5
-
58
-
-
39549123618
-
A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping
-
Liu Z, Meng J, Sun X, (2008) A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem Biophys Res Commun 368: 223-30.
-
(2008)
Biochem Biophys Res Commun
, vol.368
, pp. 223-230
-
-
Liu, Z.1
Meng, J.2
Sun, X.3
-
59
-
-
25144456056
-
Computational Cluster Validation in Post-Genomic Data Analysis
-
Handl J, Knowles J, Kell DB, (2005) Computational Cluster Validation in Post-Genomic Data Analysis. Bioinformatics 21: 3201-3212.
-
(2005)
Bioinformatics
, vol.21
, pp. 3201-3212
-
-
Handl, J.1
Knowles, J.2
Kell, D.B.3
-
60
-
-
0000122573
-
PHYLIP-Phylogeny inference package (version 3.2)
-
Felsenstein J, (1989) PHYLIP-Phylogeny inference package (version 3.2). Cladistics 5: 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
61
-
-
18644368714
-
The BioPerl Toolkit: Perl Modules for the Life Sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The BioPerl Toolkit: Perl Modules for the Life Sciences. Genome Res 12: 1611-1618.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
|