RegAnalyst

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract RegAnalyst is a valuable tool for the in silico analysis of regulatory networks.

RegAnalyst is a user-friendly web interface (server) that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) (see below…) and MycoRegDB (mycobacterial promoter and regulatory elements database).

Since ‘motif discovery’ is a challenging task, numerous tools have been developed over the past few years.

Strikingly, the existing programs were Not successful in detecting the ‘known consensus’ in all mycobacterial (epitomizing degenerate) datasets even in the absence of noise and their performance was further reduced in the presence of noise.

Consequently, MoPP, a de novo and greedy (for degeneracy) ‘inexact’ word- based tool that is tailored to enumerate ‘significantly conserved’ degenerate ‘oligonucleotide motifs’ was developed.

Benchmarking on datasets from MycoRegDB and SCPD (The Promoter Database of Saccharomyces cerevisiae) indicate that MoPP:

1) Consistently outperforms other ‘motif discovery tools’ on highly degenerate as well as less degenerate datasets; and

2) Successfully detects completely ‘degenerate motifs’ (with No two instances of a pattern being exactly the same) even in the presence of noise.

MycoRegDB --

MycoRegDB is currently one of the only available databases of ‘promoter/regulatory’ elements across various mycobacterial species [M. tuberculosis (strains H37Rv and CDC1551), M. bovis, M. leprae, M. smegmatis and M. avium subsp. paratuberculosis].

For each database entry, MycoRegDB gives a variety of useful information such as gene annotation, CDS positions, promoter/regulatory sequence [with Transcription Start Point (TSP) or binding site explicitly marked], TSP- CDS/Motif-CDS distance, and hyperlinks to reference(s).

Wherever applicable, it also provides hyperlinks to ‘gene information’ from TubercuList/BCGList/Leproma.

TubercuList --

This server is constructed around a database dedicated to the analysis of the genomes of the tubercle bacilli: TubercuList.

Its purpose is to collate and integrate various aspects of the genomic information from M. africanum, M. bovis, M. bovis BCG, M. canetti, M. microti, and above all, M. tuberculosis.

TubercuList provides a complete dataset of DNA and protein sequences derived from the paradigm strain M. tuberculosis H37Rv, linked to the relevant annotations and functional assignments.

TubercuList allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).

The manufacturer of RegAnalyst has also developed another accessory program, MyPatternFinder, that scans a given sequence or genome to find exact or ‘approximate matches’ to a ‘query motif’ of any length identified by MoPP or any other user-defined motif.

MyPatternFinder --

MyPatternFinder is a program for the detection of a ‘motif’ in a ‘DNA sequence’ by using an ‘exact search method’ (Option A) or an ‘alignment technique’ (Option B).

The user has the freedom to specify the ‘query pattern’ or select any motif from a list of ‘consensus patterns’.

In order to use the program, the user submits a ‘sequence’ in various specified formats.

The program's analysis is sent back to the user's ‘web browser’ as a single file containing information about the ‘consensus pattern’, ‘copy number’, ‘percent score’ and ‘total score’.

It also contains a link for the complete visualization of the ‘patterns detected’ in the sequence along with their positions.

PatternFinder is Not limited with respect to the size of the sequence or the pattern searched.

Note: Sequence information sent to the server is confidential and deleted after 5 days of the process being completed.

MoPP and MyPatternFinder --

The manufacturer has unambiguously proved the efficacy of MoPP:

1) In prokaryotes and lower eukaryotes;

2) In detecting motifs of various lengths;

3) In detecting highly degenerate as well as less degenerate motifs; and

4) In the presence of high noise (large sequence lengths).

Similarly, the ‘utility’ of MyPatternFinder has been shown:

1) In prokaryotes and small eukaryotic sequences;

2) In short sequences as well as complete less complex genomes; and

3) For various ‘consensus sequences’ [sigma factors, hypoxia motifs and thyroid hormone response elements (TREs)].

Thus, both MoPP and MyPatternFinder work efficiently for smaller, less complex genomes and may also be useful for ‘higher eukaryotes’ with larger, more complex genomes.

The ‘patterns detected’ using MyPatternFinder have been experimentally validated.

The detection of conserved motifs (by MoPP) and user-defined patterns of interest (by MyPatternFinder) in ‘genomic sequences’ should facilitate the understanding of ‘gene expression’ and ‘regulatory pathways’ in biological systems.

System Requirements

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Manufacturer

Manufacturer Web Site RegAnalyst

Price Contact manufacturer.

G6G Abstract Number 20583

G6G Manufacturer Number 104186