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Results: 1 to 20 of 65

1.

COMIT: identification of noncoding motifs under selection in coding sequences.

Kural D, Ding Y, Wu J, Korpi AM, Chuang JH.

Genome Biol. 2009;10(11):R133. doi: 10.1186/gb-2009-10-11-r133. Epub 2009 Nov 20.

PMID:
19930548
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica.

Jiang C, Gu X, Peterson T.

Genome Biol. 2004;5(7):R46. Epub 2004 Jun 29.

PMID:
15239831
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Computational detection of microRNAs targeting transcription factor genes in Arabidopsis thaliana.

Li X, Zhang YZ.

Comput Biol Chem. 2005 Oct;29(5):360-7. Epub 2005 Oct 10.

PMID:
16221572
[PubMed - indexed for MEDLINE]
4.

CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.

Ding Y, Lorenz WA, Chuang JH.

BMC Bioinformatics. 2012 Feb 14;13:32. doi: 10.1186/1471-2105-13-32.

PMID:
22333114
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The computational detection of functional nucleotide sequence motifs in the coding regions of organisms.

Robins H, Krasnitz M, Levine AJ.

Exp Biol Med (Maywood). 2008 Jun;233(6):665-73. doi: 10.3181/0704-MR-97. Epub 2008 Apr 11. Review.

PMID:
18408149
[PubMed - indexed for MEDLINE]
6.

Significantly lower entropy estimates for natural DNA sequences.

Loewenstern D, Yianilos PN.

J Comput Biol. 1999 Spring;6(1):125-42.

PMID:
10223669
[PubMed - indexed for MEDLINE]
7.

DNA sequence comparison considering both amino acid and nucleotide insertions/deletions because of evolution and experimental error.

Irie R, Hiraoka S, Kasahara N, Nagai K.

J Biotechnol. 1999 Mar 26;69(1):19-26.

PMID:
10201112
[PubMed - indexed for MEDLINE]
8.

A recoding method to improve the humoral immune response to an HIV DNA vaccine.

Huang Y, Krasnitz M, Rabadan R, Witten DM, Song Y, Levine AJ, Ho DD, Robins H.

PLoS One. 2008 Sep 15;3(9):e3214. doi: 10.1371/journal.pone.0003214.

PMID:
18791646
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets.

Wang XJ, Reyes JL, Chua NH, Gaasterland T.

Genome Biol. 2004;5(9):R65. Epub 2004 Aug 31.

PMID:
15345049
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

PMID:
15921531
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts.

Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A, Thermes C, d'Aubenton-Carafa Y, Crespi M.

Plant Physiol. 2006 Apr;140(4):1192-204. Epub 2006 Feb 24.

PMID:
16500993
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

How to usefully compare homologous plant genes and chromosomes as DNA sequences.

Lyons E, Freeling M.

Plant J. 2008 Feb;53(4):661-73. doi: 10.1111/j.1365-313X.2007.03326.x. Review.

PMID:
18269575
[PubMed - indexed for MEDLINE]
13.

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

Christensen OF, Hobolth A, Jensen JL.

J Comput Biol. 2005 Nov;12(9):1166-82.

PMID:
16305327
[PubMed - indexed for MEDLINE]
14.

SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins.

Edwards RJ, Davey NE, Shields DC.

PLoS One. 2007 Oct 3;2(10):e967.

PMID:
17912346
[PubMed - indexed for MEDLINE]
Free PMC Article
15.
16.

Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites.

Mulligan RM, Chang KL, Chou CC.

Mol Biol Evol. 2007 Sep;24(9):1971-81. Epub 2007 Jun 24.

PMID:
17591603
[PubMed - indexed for MEDLINE]
Free Article
17.

Computational identification of novel PR-1-type genes in Oryza sativa.

Liu Q, Xue Q.

J Genet. 2006 Dec;85(3):193-8. No abstract available.

PMID:
17406093
[PubMed - indexed for MEDLINE]
Free Article
18.

Codon evolution is governed by linear formulas.

Sorimachi K, Okayasu T.

Amino Acids. 2008 May;34(4):661-8. doi: 10.1007/s00726-007-0024-3. Epub 2008 Jan 8.

PMID:
18180868
[PubMed - indexed for MEDLINE]
19.

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.

Bonnet E, Wuyts J, Rouzé P, Van de Peer Y.

Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11511-6. Epub 2004 Jul 22. Erratum in: Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4655.

PMID:
15272084
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Rapid detection of conserved regions in protein sequences using wavelets.

Krishnan A, Li KB, Issac P.

In Silico Biol. 2004;4(2):133-48.

PMID:
15107019
[PubMed - indexed for MEDLINE]

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