Plant Proteome Response to Stress (PlantPReS)


Introduction

PlantPReS is a free proteomics database which consists of plant proteomics stress articles for searching proteins and their related stresses. It can analyze your protein accession or its sequence with whole database proteins. Also you can use PlantPReS to obtain specific protein lists based on a custom filters such as Plant, Stress (Biotic and Abiotic), Tissue, Organelle and Expression.



PlantPReS Search modes:
1- General search

This page contains several search options, which represents information after choosing one of (radio button) options such as protein, stress or plant.



Search option (Mode) Acceptable Entries
Protein UniProt accession
GI number
Protein Refseq
NCBI Gene Id
Protein name
Gene name
Stress Type of stress. i.e. "cold"
Plant Plant name. i.e. "Rice" Or "Arabidopsis thaliana"

In protein search option, if your query exists in database, database use blast for searching your query's sequence with against all sequences in database. The result will be a list that includes Identity similarity percent of target sequences against query. By this option you can find information about similar proteins to the query. In batch search only GI number or UniProt accession is acceptable and option selection is not necessary. Moreover, you can run blast for your sequences in Sequence search page for those accessions which are not available in general search.


To restrict search result in database, you can click Stress option to choose stress type or click Plant option to find records in a specific Plant organism.



2- Sequence search In this section you can search a protein sequence (amino acid type) or up to 20 protein sequences (fasta format) for blasting against all sequences in database. Like other parts of database this page creates pie charts , output file and also could e-mail result. You can also determine the similarity percentage in order to restrict blast result. Please consider, It would be better to use sequence header with the length of 20 characters or less (Optional), and at most 20 sequences can be analyzed each time.

By this part you can blast a protein sequence (amino acid) or (up to 20 fasta protein sequences) with database, Like other part of database it make Charts, Output file result and also could email result for you. You can also determine the similarity percent to limit blast scope this part applicable for the protein search by id. Please note that, It would be better to use header With length of 20 characters or less (Optional).
And at most 20 sequences can be analyzed each time.



3- Database analysis tool

This tool provides customize result by different options such as Plant, Stress, Tissue, Organelle and Expression. The analysis tool, performs multiple selection in one list which works as OR and multiple selection among different lists that works as AND as well.



4- Article search

You can search in database's article list (Proteomic stress article) by Article Title, Author(s) name, NCBI PubMed ID (PMID).


Features
1-File Output result:

In all 4 search pages, PlantPReS creates result output in a tab delimited text format or excel format (for batch searching). This file consists of protein UniProt accession, protein name, GI number, Stress, Plant, Expression, Biological process, Cellular component, Molecular function and Pubmed reference Id. You can open result files by spreadsheet program like Microsoft Excel. UniProt accession were used as accession ID for protein Id in output files and you can search those in www.UniProt.org website.


2-Charts:

PlantPReS creates 4 charts based on the frequency of tissue, organelle, plant and stress which could be seen in a graphical or text format.


3-Sequence Search:

If protein does not found in database by accession search, you can use protein Blast search (blastp) in sequence search page.


4-Batch search

In batch option, you can search up to 20 proteins (accepting only GI number or UniProt accession), or perform protein blast for up to 20 protein sequence with database.


6-Emailing result: In cases with time limitation, you can simply enter your e-mail address and PlantPReS will email the result for them.



Output information

Proteins information PrIdType (Protein Type)
PrId (Protein Accession Id)
GI Number
PrOrganism (Protein Organism in article)
PrName (Protein Name)
IdentityPercent (For Single protein search only)
SpotNo
Organelle
Tissue
SubTissue
Genotype
GenotypeDetail
Stress
StressDetail
Expression
ExpressionDetail
StageDetail
Article_PubmedID (PMID)
Gene ontology Based on Biological process, Cellular Composition and Molecular functions.
Stress Consists of number of each stress seen in result
Organelle Consists of number of each Organelle seen in result
Plant /Organism Consists of number of each Plant /Organism seen in result
Tissue Consists of number of each Tissue seen in result