I want to blast some EST with local blast. However, for some sequences, there are no matches while with the website http://www.arabidopsis.org/Blast/index.jsp.(I download the database from the site, too. so the database I used locally is same to the website.) there are do some matches found. I don't know what is the problem and how can I fix it?
I used blast 2.2.25+, built the database with this command:
makeblastdb -in TAIR10_cdna.fast -out TAIR10_cdna -dbtype nucl -input_type fasta
next I did the blast:
blastn -query buff.fa -db TAIR10_cdna -out cx274252 -dust yes -max_target_seqs 250 -penalty -3 -outfmt 4 -gapopen 5 -gapextend 2
the output like this:
BLASTN 2.2.25+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.
Database: TAIR10_cdna.fast
41,671 sequences; 64,867,051 total letters
Query= CX274252
Length=662
***** No hits found *****
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Effective search space used: 41291330612
Database: TAIR10_cdna.fast
Posted date: May 9, 2011 11:18 PM
Number of letters in database: 64,867,051
Number of sequences in database: 41,671
Matrix: blastn matrix 1 -3
Gap Penalties: Existence: 5, Extension: 2
while the results from the web ...