Workflow for Motif Identification

Summary:

The workflow identifies conserved patterns or motifs using DNA or Protein sequences as input. The input sequences are searched against a preferred database using BLAST and the significant hits obtained (orthologs) are parsed for the next step of sequence retrieval. Motif discovery programs like MEME, AlignACE, MDScan, Weeder and Consensus are used for pattern identification. The conserved regions obtained are then parsed and analyzed through a custom tool “Motif Processing Tool”.

Input files required for this workflow:

1. Protein/DNA sequence of the query for which motif identification is to be done

Standard Tools:

· BLAST

Find regions of similarity between biological sequences.

MEME:

MEME is a tool for discovering motifs in a group of related DNA or protein sequences.

· AlignACE

AlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences. It uses a Gibbs sampling strategy

· MDScan

A DNA sequence motif finding program.

· Consensus

This program determines consensus patterns in unaligned sequences.

· Weeder

Finds "Motif (transcription factor binding sites) discovery in sequences from coregulated genes of a single species.

Parsers

• GeneIDFromBLAST Parser:

This parser collects gene ids as per the required cut-offs mentioned by the user from the BLAST output and passes onto Sequence Retrieval Tool or intergenic Sequence Retrieval Tool, for which sequences are retrieved and reported in Fasta format.

• SRT to MDScan:

This parser converts the fasta format file derived from SRT/iSRT to MDScan format.

• SRT to Consensus:

This parser converts the fasta format file obtained from SRT/iSRT to Consensus format

Custom Tools

• Motif Processing Tool:

It is a custom tool which converts outputs from different motif prediction tools into a text-based visual format (for easy comparison of results). It requires output of at least two tools to compare. By default it takes first five motifs predicted by each tool. If predictions are less than five, then it takes all predicted motifs into consideration. It takes as input the outputs of different motif prediction programs and processes them to give the modified easy-to-interpret formatted output.

Usage of this tool: ./MPT -nmotifs <no_of_motifs(Max 5)> -i <Seq_input_file> -[m|meme] <meme.txt> -[a|alignace] <alignace.txt> -[c|consensus] consensus.txt>          -[s|mdscan] <MDScan.txt> -[w|weeder] <weeder.txt> -o mpt.out

Where,

-MPT is the tool

-Nmotifs is the number of motifs to be considered from each to be reported; the maximum number of motifs to be considered is 5.

-Seq_input_file is the file containing the sequences onto which the results are to be mapped

-Meme.txt is the file containing the meme output

-Alignace.txt is the file containing the alignace output

-Consensus.txt is the file containing consensus output

-MDScan.txt is the file containing MDScan output

-Weeder.txt is the file containing weeder output

-Mpt.out is the output filename

            Output of this tool:

1.      A text files containing the processed output of the motif prediction tools; giving information about the sequences, and the positions where each tool has predicted motifs to be present. Tabulated information of the same is also provided.