MotifClick – Motif Finding program

MotifClick

:: DESCRIPTION

MotifClick is a motif-finding tools

::DEVELOPER

Dr. Su’s lab at the University of North Carolina at Charlotte.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MotifClick

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 16;12:238. doi: 10.1186/1471-2105-12-238.
MotifClick: prediction of cis-regulatory binding sites via merging cliques.
Zhang S, Li S, Niu M, Pham PT, Su Z.

MOST+ 1.5 – Motif Finding system combing Genomic Sequence and Heterogenous Genome-wide Signatures

MOST+ 1.5

:: DESCRIPTION

MOST+ is a fast MOTIF finding tool(MOtif finding by Suffix tree and heterogeneous Tags). It extracts distribution features of nearby epigenomic markers, like histone modification or nucleosome occupancy, to help de novo find motif, thus rendering a higher level of accuracy on characterizing motif (cross-validated by ChIP-seq data) and more co-factors.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MOST+

:: MORE INFORMATION

Citation

BMC Genomics. 2015;16 Suppl 7:S13. doi: 10.1186/1471-2164-16-S7-S13.
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures.
Zhang Y, He Y, Zheng G, Wei C.

R’MES 3.1.0 – Finding Exceptional Motifs in Sequences

R’MES 3.1.0

:: DESCRIPTION

R’MES is a set of C++ programs devoted to the detection of motifs with an exceptional frequency in sequences (DNA, protein or other).The main question R’MES addresses is “does this motif occur in that biological sequence with an expected frequency?” In other words, can we observe it so many times, or so few times, just by chance? Usually, when the answer is no, such a motif is a candidate to have a particular biological meaning; only a candidate: statistical significance is not equivalent to biological significance.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 R’MES

:: MORE INFORMATION

Citation

Schbath, S. and Hoebeke, M. (2011).
R’MES: a tool to find motifs with a significantly unexpected frequency in biological sequences.
In Advances in genomic sequence analysis and pattern discovery (L. Elnitski, O. Piontkivska, and L. Welch, eds.). Science, Engineering, and Biology Informatics, vol. 7. World Scientific.

HapFinder 1.0 – Finding common Haplotype Blocks in a database

HapFinder 1.0

:: DESCRIPTION

HapFinder is a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.

::DEVELOPER

Singapore Genome Variation Project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package
  • Java

:: DOWNLOAD

 HapFinder

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):822-8. doi: 10.1093/bioinformatics/btr007. Epub 2011 Jan 6.
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.
Ong RT, Liu X, Poh WT, Sim X, Chia KS, Teo YY.