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Items: 1 to 20 of 357

2.
3.
4.

SIGNAL SCAN 4.0: additional databases and sequence formats.

Prestridge DS.

Comput Appl Biosci. 1996 Apr;12(2):157-60.

PMID:
8744779
5.

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.

Kel A, Tikunov Y, Voss N, Wingender E.

Bioinformatics. 2004 Jul 10;20(10):1512-6.

PMID:
15231544
6.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

7.

MATCH: A tool for searching transcription factor binding sites in DNA sequences.

Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E.

Nucleic Acids Res. 2003 Jul 1;31(13):3576-9.

8.

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

9.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

10.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

11.

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.

Corcoran DL, Feingold E, Benos PV.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

12.

SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition.

Oshchepkov DY, Vityaev EE, Grigorovich DA, Ignatieva EV, Khlebodarova TM.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12.

13.

ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T.

BMC Bioinformatics. 2008 Feb 22;9:112. doi: 10.1186/1471-2105-9-112.

14.

LASAGNA: a novel algorithm for transcription factor binding site alignment.

Lee C, Huang CH.

BMC Bioinformatics. 2013 Mar 24;14:108. doi: 10.1186/1471-2105-14-108.

15.

Context-specific independence mixture modeling for positional weight matrices.

Georgi B, Schliep A.

Bioinformatics. 2006 Jul 15;22(14):e166-73.

PMID:
16873468
16.

Annotating significant pairs of transcription factor binding sites in regulatory DNA.

Rateitschak K, Müller T, Vingron M.

In Silico Biol. 2004;4(4):479-87.

PMID:
15506997
17.

A statistical analysis of the TRANSFAC database.

Fogel GB, Weekes DG, Varga G, Dow ER, Craven AM, Harlow HB, Su EW, Onyia JE, Su C.

Biosystems. 2005 Aug;81(2):137-54.

PMID:
15941617
18.

TRANSFAC database as a bridge between sequence data libraries and biological function.

Wingender E, Karas H, Knüppel R.

Pac Symp Biocomput. 1997:477-85.

19.

Similarity of position frequency matrices for transcription factor binding sites.

Schones DE, Sumazin P, Zhang MQ.

Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19.

PMID:
15319260
20.

Transcription factor binding site identification using the self-organizing map.

Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.

Bioinformatics. 2005 May 1;21(9):1807-14. Epub 2005 Jan 12.

PMID:
15647296

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