Glycine max and Glycine soja Blast Page

BLAST query sequences against G. max and G. soja EST, GSS and CoreNucleotide sequences

Database last updated: October, 2010

View in Whole Genome Viewer ← NEWThe SoyBase Whole Genome Viewer provides a way to see all of the results of a BLAST search simultaneously on the 20 soybean chromosomes.
The HSP collapse value is the size of a region in which all HSPs will be considered to be to the same entity. The default value of 5000 is usually sufficient to collapse all HSPs in a gene (i.e. all exons found by BLASTing with a cDNA) into a single hit. Color coding is used in the genome viewer to differentiate each query in a multiple FASTA submission.
One example of how this view of the BLAST search results could be used is to determine if a group of co-expressed genes were physically clustered in the genome.
View standard BLAST report
Choose program to use and database to search:

Program

Available Databases

Enter sequence below in FASTA format

Or load it from disk
Or load an Example Sequence

Set subsequence: From To

HSP Collapse:

The query sequence is filtered for low complexity regions by default.
Filter Low complexity Mask for lookup table only

Expect
Note: other Expect values can be entered in the Other advanced options window

Advanced Options

Matrix Perform ungapped alignment

Query Genetic Codes (blastx only)

Database Genetic Codes (tblast[nx] only)

Frame shift penaltyfor blastx

Other advanced options:
NOTE: other Expect values can be entered here. For example -e 1e-17

Graphical Overview Alignment view

Descriptions Alignments Color schema

Comments and suggestions to:< the Soybase Curator>

Page Last modified: March 16, 2011
This page was based on the work of Sergei Shavirin of the NCBI