:: Center For Bioinformatics and Applied Genomics ::

no	Name	Description
1	NCBI	GenBank at the National Center of Biotechnology Information, National Library of Medicine, Washington, DC
2	EMBL	European Molecular Biology Laboratory (EMBL) Outstation at Hixton, England
3	DDBJ	DNA DataBank of Japan (DDBJ) at Mishima, Japan
4	PIR	Protein International Resource (PIR) database at the National Biomedical Research Foundation in Washington, DC
5	SwissProt	The SwissProt protein sequence database at ISREC, Swiss Institute for Experimental Cancer Research in Epalinges/Lausanne
6	SRS	The Sequence Retrieval System (SRS) at the European Bioinformatics Institute allows both simple and complex concurrent searches of one or more sequence databases.
7	Bayes block aligner	Zhu et al. (1998)
8	BCM Search Launcher: Pairwise sequence alignment	see Web site
9	SIMMLocal similarity program for finding alternative alignments	Huang et al. (1990); Huang and Miller (1991); Pearson and Miller (1992)
10	Global alignment programs (GAP, NAP)	Huang (1994)
11	FASTA program suite	Pearson and Miller (1992); Pearson (1996)
12	BLAST 2 sequence alignment (BLASTN, BLASTP)	Altschul et al. (1990)
13	Likelihood-weighted sequence alignment (lwa)	see Web site
14	CLUSTALW or CLUSTALX	Thompson et al. (1994a, 1997); Higgins et al. (1996)
15	MSA	Lipman et al. (1989);Gupta et al. (1995)
16	PRALINE	Heringa (1999)
17	DIALIGN segment alignment	Morgenstern et al. (1996)
18	Parallel PRRN progressive global alignment	Gotoh (1996)
19	SAGA genetic algorithm	Notredame and Higgins (1996)
20	Aligned Segment Statistical Evaluation Tool (Asset)	Neuwald and Green (1994)
21	BLOCKS Web site	Henikoff and Henikoff (1991, 1992)
22	eMOTIF Web server	Nevill-Manning et al. (1998)
23	GIBBS, the Gibbs sampler statistical method	Lawrence et al. (1993); Liu et al. (1995); Neuwald et al. (1995)
24	HMMER hidden Markov model software	Eddy (1998)
25	MACAW, a workbench for multiple alignment construction and analysis	Schuler et al. (1991)
26	MEME Web site, expectation maximization method	Bailey and Elkan (1995); Grundy et al. (1996, 1997); Bailey and Gribskov (1998)
27	Profile analysis at UCSD	Gribskov and Veretnik (1996)
28	SAM hidden Markov model Web site	Krogh et al. (1994); Hughey and Krogh (1996)
29	MultAlin	Corpet (1988)
30	RNA secondary structures, Group I introns, 16S rRNA, 23S rRNA	Gutell (1994); Schnare et al. (1996 and references therein)
31	RNA structure database	see Web page
32	RNA world at IMB Jena	S?hnel (1997)
33	rRNAADatabase of ribosomal subunit sequences	De Rijk et al. (1992, 1999)
34	Signal recognition particle database	Samuelsson and Zwieb (2000)
35	Small RNA database	see Web page
36	snoRNA database for S. cerevisiae	Lowe and Eddy (1999)
37	tmRNAa database	Wower and Zwieb (1999)
38	tmRNAa Web site	Williams (1999)
39	tRNAscan-SE search server	Lowe and Eddy (1997)
40	tRNA and tRNA gene sequences	Sprinzl et al. (1998)
41	uRNA database	Zwieb (1997)
42	Vienna RNA package for RNA secondary structure prediction and comparison	Hofacker et al. (1998); Wuchty et al. (1999)
43	Viroid and viroid-like RNA sequences	Lafontaine et al. (1999)
44	Entrez	taxonomically related structures or group of organisms
45	RDP (Ribosomal database project)	ribosomal RNA-derived trees
46	Tree of life	information about phylogeny and biodiversity
47	FASTA (TFASTA), SSEARCH	list of database sequences having the most significant similarity scores
48	BLASTP (TBLASTN)	list of database sequences having the most significant similarity scores
49	WU-BLAST	list of database sequences having the most significant similarity scores
50	PROFILESEARCH	list of database sequences that can be aligned with the profile
51	MAST	list of database sequences with one or more patterns represented by PSSM but not necessarily in the same order
52	PSI- BLAST	PSI-BLAST finds a set of sequences related to each other by the presence of common patterns
53	PROSITE	list of sequence patterns found in query sequence
54	PFAM	list of sequence patterns found in query sequence
55	CDD/IMPALA	list of sequence patterns found in query sequence
56	BLASTTBasic Local Alignment Search Tool	Altschul et al. (1990, 1997) Altschul and Gish (1996)
57	WU-BLAST	Altschul et al. (1990, 1997);Altschul and Gish (1996)
58	FASTA	Pearson (1995, 1996, 1998, 2000)
59	BCM Search Launcher (Baylor College of Medicine)	see Web site
60	TIGR gene indices search	see Web site
61	BCM Search Launcher (with programming links to several servers)	Baylor College of Medicine
62	bic-sw	Bic server European Bioinformatics Institute
63	MPsearch	National Institute of Agrobiological Resources, Tsukuba, Japan
64	Scanps	G.Barton, European Bioinformatics Institute
65	SSEARCH E-mail server	DNA Databank of Japan
66	Swat	Phil Green, University of Washington
67	EMOTIF Scan	SwissProt and Genpept
68	Prosite patterns	SwissProt and TrEMBL
69	ISREC pattern-finding	SwissProt and non-redundant EMBL database
70	fpat	PDB SwissProt Genpept
71	PHI-BLAST	BLAST databases
72	MOTIF	SwissProt, PDB, PIR, PRF, Genes
73	BLOCKS	most databases
74	MAST	most databases
75	BLIMPS	locally available databases
76	Probe	locally available databases
77	Genefind	PIR
78	Profilesearch	locally available databases
79	Profile-SS	most databases
80	Arabidopis intron splice site table	see Web site
81	Codon usage database	see Web site
82	Ecoparse for finding E. coli genes based on HMM model	Krogh et al. (1994)
83	EST-GENOME for alignment of EST/cDNA and genomic sequences	see Web site; also see Florea et al. (1998)
84	Exon recognizer including GeneScope	see Web page
85	FGENES and related programs that use linear discriminant analysis or hidden Markov modelsa	Solovyev et al. (1995); see Web site
86	FINEXXexon intron boundary analysis	Brown et al. (1995)
87	GeneFinder access site at the Sanger Center	collection of methods
88	Genehacker for microbial genomes based on HMMs	Hirosawa et al. (1997)
89	GeneID-3 Web server using rule-based models and GeneID+	Guig? et al. (1992); Guig? (1998)
90	GeneMark and GeneMark.hmmc uses hidden Markov models	Lukashin and Borodovsky (1998)
91	GeneMark home page (see webgenemark)	Borodovsky and McIninch (1993)
92	GeneParsera Web page uses combination of neural network and dynamic programming methods	Snyder and Stormo (1993
93	Genescan using Fourier transform of DNA sequences to find characteristic patterns	Tiwari et al. (1997)
94	GeneScope	Murakami and Takagi (1998)
95	Genetic code variations	see Web site
96	Genie for finding human genes in 10-kb DNAs and in Drosophila by hidden Markov models and neural networks	Kulp et al. (1996); Reese et al. (1997
97	GenLang using linguistic methods	Dong and Searls (1994)
98	GenScan based on probabilistic model of gene structure for vertebrate Drosophila and plant genes	Burge and Karlin (1998)
99	Genseqer for aligning genomic and EST sequences	see Web site and SplicePredictor
100	Glimmer uses interpolated Markov models for prokaryotic translation	Salzberg et al. (1998)
101	GrailII prediction by neural networks based on scores of characteristic sequence patterns and composition	Uberbacher and Mural (1991); Uberbacher et al. (1996)
102	Hexon for exon prediction by linear discriminant analysis	Solovyev et al. (1994)
103	Human splice sites with decision tree analysisd	Thanaraj (1999)
104	INFO for finding splice junctions by database similarity search	Laub and Smith (1998)
105	INFOGENE: a database of known gene structures and predicted genes	Solovyev and Salamov (1999)
106	Initiation codon analysis	see Web site
107	Microbial genome coding region identification based on Markov chains of order 5	Audic and Claverie (1998)
108	Morgan for finding vertebrate genes by decision tree classificationd	Salzberg (1998); Searls (1998)
109	MZEF uses quadratic discriminant analysis for human, mouse, Arabidopsis and S. pombe exons	Zhang (1997)
110	NetGene uses neural networks for analysis of splice sites in human C. elegans and Arabidopsis genes	Brunak et al. (1991); Hebsgaard et al. (1996)
111	NetPlantGene	see NetGene
112	NetStart uses neural networks for gene prediction in vertebrate and Arabidopsis genes	Pedersen and Nielsen (1997)
113	Procrustes based on comparison of related genomic sequences	Gelfand et al. (1996)
114	Push-button Gene Finder for gene identification using Markov and hidden Markov models	see Web site
115	SplicePredictor for plants uses trained logitlinear models	Brendel and Kleffe (1998); Brendel et al. (1998)
116	Splicing Sites by neural network at LBNL	see Genie
117	Translate tool at ExPASy	see Web site
118	Translation machine on the Web at EBI	see Web site
119	Translation of large genome sequences on the Web	see Web site
120	Veil (Viterbi exon-intron locator) uses hidden Markov models for vertebrate DNA	Henderson et al. (1997)
121	Webgene a set of gene prediction tools and concurrent database similarity searches	see Web site
122	Webgenemark and Webgenemark.hmmc	see GeneMark; Lukashin and Borodovsky (1998)
123	Yeast splice sites by M. Ares Jr. laboratory	Spingola et al. (1999)
124	ConsInspector-see Transfac databasea
125	Core-Promoter-for finding RNAPII promoters of human genes by quadratic discriminant analysis	Zhang (1998a, b)
126	EPD Eukaryotic promoter database	Bucher (1990); Prier et al. (1999, 2000)
127	EpoDB genes expressed during vertebrate erythropoiesis	Stoeckert et al. (1999)
128	FastM for transcription factor binding sites	Klingenhoff et al. (1999)
129	GeneExpress analysis of transcriptional regulations with TRRD database	Kolchanov et al. (1999a, b)
130	Genome inspector for combined analysis of multiple signals in genomes	Quandt et al. (1997)
131	GrailII prediction of TSS by neural networks based on scores of characteristic sequence patterns and composition	Uberbacher and Mural (1991); Uberbacher et al. (1996)
132	MAR-FINDER for finding matrix attachment regions	Kramer et al. (1997); Singh et al. (1997)
133	MatInspector
134	Nuclear (including glucocorticoid) receptor resource	Martinez et al. (1997)
135	Mirage (Molecular Informatics Resource for the Analysis of Gene Expression)	see Web page
136	NNPP Promoter Prediction by Neural Network for prokaryotes or eukaryotes	Reese et al. (1996)
137	NSITE-search for TF binding sites or other consensus regulatory sequences	see Web site
138	OOTFD Object-Oriented Transcription Factor Database	Ghosh (1998)
139	PLACE plant cis-acting regulatory elements	Higo et al. (1999)
140	PlantCARE plants cis-acting regulatory elements	Rombauts et al. (1999)
141	Pol3scan for RNAP III/tRNA promoter sequences using pattern scoring matrices	Pavesi et al. (1994)
142	Polyadq for locating polyadenylation sites	Tabaska and Zhang (1999)
143	Promoter element weight matrices and HMMs	Bucher (1990)
144	Promoter II for recognition of PolII sequences by neural networks	Knudsen (1999)
145	PromoterScane	Prestridge (1995) and see Web site
146	RegScan for promoter classification	Babenko et al. (1999)
147	Sequence walkers for graphical viewing of the interaction of regulatory protein with DNA binding site	Schneider (1997)
148	Signal scan for transcriptional elements	Prestridge (1991, 1996)
149	TargetFinder for promoter searching in selected annotated sequences	Lavorgna et al. (1999)
150	TESS for searching for transcription factor binding sites	Schug and Overton (1997a, b)
151	Tfbind for transcription factor binding sites	Tsunoda and Takagi (1999)
152	Thyroid receptor resourcec	see Web page
153	Transfac programs providing search for TF binding sites. MatInd for making scoring matrices and MatInspector for searching for matches to matrices	Kn?ppel et al. (1994);Quandt et al. (1995);Heinemeyer et al. (1999);Klingenhoff et al. (1999)
154	TRRD transcriptional regulatory region database; see GeneExpress	Kolchanov et al. (1999a)
155	TSSG, like TSSW but based on sequences from a different promoter database	see Web site
156	TSSW; recognition of human PolII promoter region and start of transcription by linear discriminant function analysis	see Web site
157	Yeast cell cycle gene retrieval and promoter analysis	Wolfsberg et al. (1999)
158	Yeast cell cycle analysis project	Spellman et al. (1998)