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Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.

Kingsford CL, Ayanbule K, Salzberg SL.

Genome Biol. 2007;8(2):R22.PMID: 17313685 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of transcriptional terminators in Bacillus subtilis and related species.

de Hoon MJ, Makita Y, Nakai K, Miyano S.

PLoS Comput Biol. 2005 Aug;1(3):e25. Epub 2005 Aug 12.PMID: 16110342 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of transcription terminators in bacterial genomes.

Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL.

J Mol Biol. 2000 Aug 4;301(1):27-33.PMID: 10926490 [PubMed - indexed for MEDLINE]Related articles

Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures.

d'Aubenton Carafa Y, Brody E, Thermes C.

J Mol Biol. 1990 Dec 20;216(4):835-58.PMID: 1702475 [PubMed - indexed for MEDLINE]Related articles

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes.

Livny J, Fogel MA, Davis BM, Waldor MK.

Nucleic Acids Res. 2005 Jul 26;33(13):4096-105. Print 2005.PMID: 16049021 [PubMed - indexed for MEDLINE]Related articlesFree article

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.

Livny J, Teonadi H, Livny M, Waldor MK.

PLoS One. 2008 Sep 12;3(9):e3197. Erratum in: PLoS ONE. 2008;3(11). doi: 10.1371/annotation/a03e1870-1dd7-4c16-8c46-2268eeb2a50a. PMID: 18787707 [PubMed - indexed for MEDLINE]Related articlesFree article

Occurrence, divergence and evolution of intrinsic terminators across eubacteria.

Mitra A, Angamuthu K, Jayashree HV, Nagaraja V.

Genomics. 2009 Aug;94(2):110-6. Epub 2009 Apr 23.PMID: 19393739 [PubMed - indexed for MEDLINE]Related articles

Conserved economics of transcription termination in eubacteria.

Unniraman S, Prakash R, Nagaraja V.

Nucleic Acids Res. 2002 Feb 1;30(3):675-84.PMID: 11809879 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of rho-independent transcriptional terminators in Escherichia coli.

Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, Ecker DJ.

Nucleic Acids Res. 2001 Sep 1;29(17):3583-94.PMID: 11522828 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium.

Mitra A, Angamuthu K, Nagaraja V.

Tuberculosis (Edinb). 2008 Nov;88(6):566-75. Epub 2008 Sep 3.PMID: 18768372 [PubMed - indexed for MEDLINE]Related articles

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

BMC Genomics. 2008 Feb 28;9:106.PMID: 18307801 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA.

Nardone J, Lee DU, Ansel KM, Rao A.

Nat Immunol. 2004 Aug;5(8):768-74. Review.PMID: 15282556 [PubMed - indexed for MEDLINE]Related articles

Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them.

Brendel V, Hamm GH, Trifonov EN.

J Biomol Struct Dyn. 1986 Feb;3(4):705-23.PMID: 3078109 [PubMed - indexed for MEDLINE]Related articles

A computer algorithm for testing potential prokaryotic terminators.

Brendel V, Trifonov EN.

Nucleic Acids Res. 1984 May 25;12(10):4411-27.PMID: 6374619 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination.

Washio T, Sasayama J, Tomita M.

Nucleic Acids Res. 1998 Dec 1;26(23):5456-63.PMID: 9826772 [PubMed - indexed for MEDLINE]Related articlesFree article

A clustering method for repeat analysis in DNA sequences.

Volfovsky N, Haas BJ, Salzberg SL.

Genome Biol. 2001;2(8):RESEARCH0027. Epub 2001 Aug 1.PMID: 11532211 [PubMed - indexed for MEDLINE]Related articlesFree article

In silico characterization of DNA motifs with particular reference to promoters and terminators.

Lavigne R, Villegas A, Kropinksi AM.

Methods Mol Biol. 2009;502:113-29.PMID: 19082554 [PubMed - indexed for MEDLINE]Related articles

A predictive model for identifying mini-regulatory modules in the mouse genome.

Yaragatti M, Sandler T, Ungar L.

Bioinformatics. 2009 Feb 1;25(3):353-7. Epub 2008 Dec 3.PMID: 19052060 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast algorithms for large-scale genome alignment and comparison.

Delcher AL, Phillippy A, Carlton J, Salzberg SL.

Nucleic Acids Res. 2002 Jun 1;30(11):2478-83.PMID: 12034836 [PubMed - indexed for MEDLINE]Related articlesFree article

New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators.

Ambur OH, Frye SA, Tønjum T.

J Bacteriol. 2007 Mar;189(5):2077-85. Epub 2006 Dec 28.PMID: 17194793 [PubMed - indexed for MEDLINE]Related articlesFree article