Python BLAST info viewer
Alexander Kozik and Brian Chan
Python BLAST Info Viewer is designed to view results of BLASTX search
of the set of ESTs (or contigs) against Arabidopsis predicted proteins. The viewer
displays graphical alignments for the first three best hits (if found) from BLAST
report as well as intron-exon positions for Arabidopsis protein sequence.
Viewer interface:
Input files:
Three input files are required to run the viewer:
-
BLAST Info2 file. This file is derived by parsing of BLAST output by
tcl_blast_parser.
Default info2 file of this version of the viewer is
x-let-ath-blastX.info2
(info2 file of the BLASTX search of the lettuce EST assembly against
Arabidopsis predicted proteins).
-
Genome Coordinates file. This file is derived by parsing of the Arabidopsis GenBank
files using Python GenBank parser.
This file contains coordinates for all genes of the Arabidopsis genome together with their coordinates
for introns and exons.
x-ath_NCBI_genes.coords.nr
is a tab-delimited file, first column contains gene IDs, last column - intron/exon positions.
-
Sequence file. This tab-delimited file contains DNA sequences corresponding to
the Query set of the BLASTX report. Default set is a
lettuce EST assembly from
CGPDB.
Program operation:
Select three types of input files described above (or agree with default names if
you work with lettuce assembly). Click on Load All button, wait until all
three files are loaded into memory. Then select contig ID or singleton ID of the
sequence you like to analyze (Query ID entry) and click on corresponding
Search button. Two new windows should appear displaying the alignment and
corresponding DNA sequence. Change value "1" to "2" on the Hit N entry
window and click Search button again. Graphical display for the second
BLAST hit should appear. You can view alignments for the fist three best hits
only.
The top bar of the alignment is a Arabidopsis protein sequence. The bottom bar is
a EST sequence or contig. Overlap of the alignment is displayed in yellow (Arabidopsis)
and green (EST query). Non-match regions are shown in blue. Intron positions in
Arabidopsis sequence are shown by red triangles. Note, that all values are shown in
nucleotides. If value is shown in amino acids the "aa" suffix is added to that value.
Examples of graphical display for contig QG_CA_Contig1258:
Note, that EST sequence could have reverse orientation to Arabidopsis protein. In this case you
can see label R on the right side of EST bar. At the same time, regardless of forward/reverse
BLAST orientation, sequence in the text window is always in forward orientation. Yellow color highlights
portion of sequence corresponding to the alignment. Labels R or F of the Arabidopsis sequence
correspond to Watson/Crick orientation of the gene on the genomic sequence and have nothing to do
with orientation of the sequence in the BLAST report.
Download the program and example input files:
Python interpreter. You need to install it to run the viewer.
x-BlastSearchViewer_Aug_26_2003.py the viewer source code.
x-ath_NCBI_genes.coords.nr Arabidopsis genome coordinates.
x-let-ath-blastX.info2 Info2 file (lettuce set).
x-lettuce_assembly.tab Lettuce EST sequences (tab-delimited format)
x-sun-ath-blastX.info2 Info2 file (sunflower set).
x-sunflower_assembly.tab Sunflower EST sequences (tab-delimited format)
Feedback:
email: Alexander Kozik
last modified: February 05 2004