In Silico Gene Bank for Adaptation to Abiotic Stresses
The abundance of sequence information of transcripts implicated in abiotic stress responses in different plant species necessitates integration of available DNA and protein sequence information for enabling exhaustive bioinformatic analyses. Towards this aim, In Silico Gene bank for Plant Adaptation to Abiotic Stresses (IGBAAS) was developed and linked to online bioinformatic tools. The different search options, analytical tools and interactive features present in the database are described below.
The abiotic stress tolerant genes can be searched in this database using key words like plant name, gene name or stress type. All the three can be used for narrow search and any of them can be used for wide search.
The results will be displayed in a new page with the description of each sequence and the IGBAAS No has link to information regarding each sequence. This page also has link to PubMed and Wiki genes for the keyword.
A check box is present for each sequence, which can be used to get the FASTA format of selected genes for bioinformatic analysis using the button “GetFASTA” . A new page containing the FASTA format of the sequences will appear.
Details of each sequence can be obtained by clicking the IGBAAS No of respective sequences. A separate menu bar is present which has options for viewing the Fasta format of the sequence. The complete gene information can be viewed by selecting the gene info tab. This page also has link to primer design, siRNA design and BLAST for that sequence. This page also have connectivity to the NCBI page of the respective gene sequence. By selecting the protein id, user can have direct access to the respective protein information of that particular gene.
The protein sequences of genes which are activated during abiotic stress can also be searched using this database. The search can be carried out using the keywords like plant name, gene name or stress type. The total results of the search will be displayed in a new page. The sequences can be selected by clicking the check box provided to each sequences for multiple alignment.
Degenerate Primer Search
The degenerate primers for ion transporter genes cited in different literatures can be searched by giving the gene name. It also has the link to the respective literature. This database is an interactive database, where we encourage the users to update available primer sequences in this database.
IGBAAS allows the user to search different labs which are working on salinity and also has links to several bioinformatics tools in the main tab “Links”.
We classified the genes implicated in abiotic stresses according to their function and made a flowchart with link to access the respective gene sequence information. This can be accessed using the user friendly classification.
For a quick search, different classifications of abiotic stress genes are given in the left side bar.
Uploading new information
Abiotic-stress tolerance is multigenic and studies on abiotic stress response in different plant systems have resulted in the identification of a large number of genes implicated in abiotic stress responses. This database is an initiative to integrate molecular information's concerning abiotic stresses in plants.
IGBAAS is an interactive database, enables users to update the information’s regarding nucleotide and protein sequences and degenerate primers which are not available in the database.
To upload a new information to the database a user needs to register with IGBAAS. Registering with IGBAAS is a quick process, needs basic information about the user. We ask the users to take care while typing Email address and Date of Birth as Email address is the userid for login and Date of Birth is needed to regain the password if lost. We also ask the users to use different password other than which you use for Email. The link to registration page is present in the login page.
The users can Login to the databse using the Email id and the password used while registration.
The users who can only provide a hint on new data can provide data as new gene name or a new sequence information in NCBI as their accession number by this option. The details regarding the information provided by the user will be updated by the database team as soon as possible and will be informed.
The users who can help the database by providing complete information regarding a new sequence information can update the database using this option. This has four continuous pages and needs to complete all the fields. First two pages for nucleotide sequence information and next two pages for protein sequence information. If a particular nucleotide sequence don’t have corresponding protein sequence, users are asked to fill all the fields in the protein pages as “Nil”.