Web server for TFBS PFM database search using PFV algorithm

This web interface is to demonstrate the effectiveness of our PFV algorithm for PFM searching and retrieval
Paper is submitted to Bioinformatics for peer review

 

Supported input formats:

Example inputs
Formats

TRANSFAC

The standard TRANSFAC format. Our input parser will read the lines begining with NA, PO, all the lines begining with numbers and the last XX line. Multiple PFMs in one query is supported.

TRANSFAC (simple styple)

A simplified version of TRANSFAC format. Our input parser will read the lines begining with DE, all the lines begining with numbers and the last XX line. Please also keep the last X in each line with numbers. Multiple PFMs in one query is supported.

JASPAR

The format used in JASPAR database. Our input parser will read all the five lines for each PFM. The PFM name must followed by '>' at the begining of each input PFM. Multiple PFMs in one query is supported.

FASTA (multiple sequence alignment)

The FASTA format input containing all the motif sequences making up one single PFM. Our input parser will not read anything after the '>' but do keep the '>' to make it a FASTA format input. The sequences could be in either upper or lower case, but must sure the sequence only contains the 4 types of bases. Gap in sequence is also not allowed. Multiple PFMs in one query is NOT supported. Therefore, please make sure all the sequences have the same length. If not, they will be treated as different 'consensus sequences'. (see below)

FASTA (consensus sequences)

The FASTA format input containing consensus motif sequence(s). Our input parser will read anything after the '>' as the query PFM's name. The sequences could be in either upper or lower case, but must sure the sequence only contains the allow characters as specified here. Multiple consensus sequences in one query is supported.

   

 

 

Web server maintained by
Minli Xu (mxu5@uncc.edu) & Dr Zhengchang Su (zcsu@uncc.edu)
Bioinformatics Research Center, University of North Carolina - Charlotte
Last update: 18-May-2009 5:22 PM