GoFish 1.11alpha – Find Genes with Combinations of Gene Ontology Attributes

GoFish 1.11alpha

:: DESCRIPTION

GoFish  selects a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GoFish

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Apr 12;19(6):788-9.
GoFish finds genes with combinations of Gene Ontology attributes.
Berriz GF, White JV, King OD, Roth FP.

REMOCOD – REgulatory MOtif COmbination Detector

REMOCOD

:: DESCRIPTION

REMOCOD  is a program for the systematic identification of pairs of transcription factor binding sites (TFBSs) that tend to co-occur in promoter sequences of a set of co-regulated genes. Given a set of gene IDs, the program first detects over-represented TFBSs in the promoter sequences corresponding to these genes, and subsequently predicts regulatory motifs that show a tendency to co-occur with any of the over-represented TFBSs.

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Vandenbon A, Kumagai Y, Akira S, Standley DM.
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription“,
BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11

IPCA-CMI – Inferring Gene Regulatory Networks based on Combination of PCA-CMI and MIT score

IPCA-CMI

:: DESCRIPTION

IPCA-CMI is an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 IPCA-CMI

:: MORE INFORMATION

Citation

PLoS One. 2014 Apr 11;9(4):e92600. doi: 10.1371/journal.pone.0092600. eCollection 2014.
IPCA-CMI: an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.
Aghdam R1, Ganjali M1, Eslahchi C

OCSANA – Optimal Combinations of Interventions from Network Analysis

OCSANA

:: DESCRIPTION

OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

OCSANA

:: REQUIREMENTS

:: DOWNLOAD

 OCSANA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.
OCSANA: optimal combinations of interventions from network analysis.
Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

tacg 4.1.0 – Finds Short Patterns and Specific Combinations of Patterns in Biological Strings

tacg 4.1.0

:: DESCRIPTION

tacg is a command-line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms a core of the program, it has been expanded to fill more roles, sort of a ‘grep’ for DNA.

::DEVELOPER

Harry Mangalam <harry.mangalam@uci.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 tacg

:: MORE INFORMATION

Citation

tacg–a grep for DNA.
Mangalam HJ.
BMC Bioinformatics. 2002;3:8. Epub 2002 Mar 6.

find_max_cover – Determine the best Combination of Local Alignments to a Query Sequence

find_max_cover

:: DESCRIPTION

find_max_cover  (FindMaxCover) finds the combination of local alignments that covers the maximum number of residues in a query sequence.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 find_max_cover

:: MORE INFORMATION

Citation

Conant, G. C., and A. Wagner, (2004)
A fast algorithm for determining the best combination of local alignments to a query sequence,
BMC Bioinformatics, 5: 62.