Glycine max and Glycine soja Blast Page

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

View in Whole Genome Viewer The 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 Download FASTA of selected database.

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

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA

U.S. Public Domain