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Blastp-2.6.0+

Blastp-2.6.0+

Jun 21, 2017

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Rationale and Background

Blastp-2.6.0+ compares an amino acid query sequence against a protein sequence database. The program aligns sequence (input file) on the base prepared by program makeblastdb.

Mandatory arguments

  • Inputs: Path to the query file name. Amino acid file in fasta format

  • Database: Path to the Database folder prepared by makeblastdb

  • Output File Name: The name of the final output file


Parameters

  • e-value:Expect value (E) for saving hits (Default is 10.0)

  • Output Format: Format of the output file (Default is "flat query anchored with identities")

  • Option1 and Option2 are your favorite additional blastp parameters that you want to specify. For example if you want to keep only one best bit out of several many hits for the same query id then you put -num_alignments 1 in the Option1 box. For more details about Blastp parameters please visit Blast documentation page here

Test Run

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > blastp (/iplant/home/shared/iplantcollaborative/example_data/blastp)

Mandatory arguments: 

  • Inputs: BAtestpep.fa

  • Database: refseq_protein

  • Output File Name: final_out.txt

Parameters:

  • e-value: 10.0 (Default)

  • Output Format: "flat query anchored with identities" (Default)

  • Option1: num_alignments 1

Output

  • final_out.txt