Help

This page is designed to guide users about using PVsiRNAdb. It constitutes of various snapshots of various procedures, facilities and understading the output.


Search Browse Tools
Simple Search Browse by Virus Name BLAST
Batch Search Browse by Plant Name SW Align
Browse by PubMed Id Mapping




Search




Simple Search

This is a very simple and easy search option. User can search any query in any of the fields (e.g. Plant Nicotiana Benthamiana).Results will be displayed according to the selected fields to be dispalyed. e.g. Virus, Sequence, PMID etc.

1. Default Condition


2. When clicked on "Containing"


3. When clicked on "Exact"








Batch Search

This is a level-up part of search option. User can search multiple queries in any of the fields (e.g. Plant , Virus and PubMed Id).All the results matching to the queries will be displayed with all the information available.

1. Search by "Plant Name"


2. Search by "Virus Name"


3. Search by "PubMed Id








Browse




Browse by Virus Name

This interface allows the user to browse all the virus specific siRNAs available in PVsiRNAdb. All the available information will be dispalyed e.g. Virus, Sequence, PMID etc.









Browse by Plant Name

This interface allows the user to browse all the plant specific siRNAs available in PVsiRNAdb. All the available information will be dispalyed e.g. Virus, Sequence, PMID etc.









Browse by PubMed ID

This interface allows the user to browse all siRNAs available in PVsiRNAdb fetched from specific PubMed ID. All the available information will be dispalyed e.g. Virus, Sequence, PMID et











Tools




BLAST

User can run a BLAST search for sequences. The server provides options to BLAST against a specific type of virus's siRNA or against whole PVsiRNA database. Different E-values are provided , from which user can choose one. Default E-value is set at 10









SW align

SW align i.e. Smith-Waterman Alignment page assists the user to run a Local alignment of a sequence using Smith-Waterman algorithm. User can align a sequence either against the reference genome of specific virus or against the reference genome of all the virus available in PvsiRNAdb OR user can align a sequence against the siRNAs of specific virus or all virus data present in PVsiRNA database.

1. Alignment against reference genome of virus



2. Alignment against siRNAs of virus






Mapping

This module maps the PVsiRNAdb siRNA's on the user provided nucleotide sequence. Mapping can be done against different specific virus's siRNAs or all the siRNAs available in PVsiRNAdb. Different E-value can be provided for mapping.





Dr. Shailesh Kumar                 SK Lab                 NIPGR                  DBT                  © 2018 Shailesh Lab.