CTF 0.91 – CRF-based Transcription Factor Binding Sites Finding System

CTF 0.91

:: DESCRIPTION

CTF is a conditional random field (CRF)based transcript factor binding site (TFBS) finding system.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CTF

:: MORE INFORMATION

Citation:

BMC Genomics. 2012;13 Suppl 8:S18. doi: 10.1186/1471-2164-13-S8-S18. Epub 2012 Dec 17.
CTF: a CRF-based transcription factor binding sites finding system.
He Y1, Zhang Y, Zheng G, Wei C.

CNetQ / Corbi 0.2-5 – Network Querying tool based on Conditional Random Fields

CNetQ / Corbi 0.2-5

:: DESCRIPTION

CNetQ is an network querying tool based on conditional random fields.A large amount of biomolecular network data for multiple species have been generated by high-throughput experimental techniques, including undirected and directed networks such as protein-protein interaction networks, gene regulatory networks and metabolic networks. There are many conserved functionally similar modules and pathways among multiple biomolecular networks in different species, therefore, it is important to analyze the similarity between the biomolecular networks. Network querying approaches can efficiently discover the similar subnetworks among different species. However, many existing methods only partially solve this problem. A novel approach for network querying problem based on conditional random fields (CRF) model is proposed, which can handle both undirected and directed networks, acyclic and cyclic networks, and any number of insertions/deletions. The CRF method is fast and can query pathways in a large network in seconds using a PC.

CNetQ Online Version

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

   CNetQ / Corbi

:: MORE INFORMATION

Citation

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang.
An Efficient Network Querying Method Based on Conditional Random Fields.
Bioinformatics, 27 (22): 3173-3178, 2011. doi: 10.1093/bioinformatics/btr524.