Molecular biology (Wet-lab):
We are trying to identify potential biomarkers to aid in drug target identification and facilitate drug discovery. The overall strategy involves both in silico and in vitro studies, and the wet-lab experiments support our in-silico methods. We intend to characterize alternatively spliced forms, particularly from the mammalian testis tissue. The wet-lab techniques used are microarray, molecular cloning, sequencing and real-time PCR. We are also validating some of the related bioinformatics resources using the same methods. These non-commercial research experiments are performed in collaboration with IBAB.

Dry-lab:


In collaboration with IBAB, gene expression analysis is being performed in specific mammalian tissues for identifying diseases markers. The following free tools and databases are also being developed:

Tools

Oligo-junction:
This new primer designing tool is being developed after some a thorough comparative analysis of existing primer designing tools. Several areas not addressed by the already existing tools will be attended to in this suite.

Hit-Sorter:
A literature search tool is being developed, using PERL language, to facilitate the PubMed usage.

Mot-Det:
A software is being developed to detect presence of patterns of short nucleotide sequences or motifs within one or more sequences submitted. The program can identify a) specific pattern, b) variants of a consensus pattern or c) most common patterns in the given sequence or a set of sequences. The program can also identify the patterns within different blocks of the sequences.

Databases/platforms:
Shodhaka is collaborating with the IBAB team to develop highly reliable tissue-specific and disease-specific platforms, which can help to obtain highly reliable expression patterns of genes in different conditions of the tissues and to cluster the genes or promoters based on the expression characters.

Miscellaneous:
All these programs are not yet available for public use. You can send a request if interested.

Oligo-Tracer:
It can detect even part of the short query sequence in a bigger sequence submitted.

Oligo-number :
Numbers the nucleotides if a sequence is submitted.

List-Matcher:
With 2 or more lists of any terms, gene names - for example, the tool classifies the terms into those which are unique to each list vs. those common to multiple lists.