Tools and Databases

Tools/programs
- Exprimer: A web based application to design primers from exon junctions.

- Primer junction: Currently the Ex-primer has been improved and this new comprehensive tool is under test. This program is available on request for academic purposes (please send in your request to info@ibab.ac.in with your name, designation and affiliation; also add in the subject: Attention to Dr. Kshitish).

- PERLit: A literature search tool developed, using PERL language, to facilitate the PubMed usage. The tool also aids creation of a quick database which can be further searched using the program.
"This program is not yet available for public use. You can send a request by registering."

- Mot-Det: A software 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.
"This program is not yet available for public use. You can send a request by registering."

- 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

- Gen-sum: Gene summary extractor: With any gene name as input, the tool retrieves basic information, including the synonyms, sequence, potential promoter, TSS etc

- 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

Databases:
- MGEXdb: A database of transcriptional elements of co-regulated genes, with manual curation of the data.
"This program is not yet available for public use. You can send a request by registering."

Articles and supplementary materials of published literature

1. Kshitish Acharya K. (2006) The biotech-bioinfo interface in the context of education and growth of the biotechnology industry in India today. Biovistas 1(1): 7-13. Click here to access the full article.

Publications