blastall problem - blast (Mar/25/2007 )

hello~

i use stand alone blast in linux (fedora core)

and i tried to blastall for blast (x, n )

run that kind option for blast

"blastall -p blastx -d nr -i aaa.fas -e 5 -F F -o aaa.out -v 10 -a 3"

and then if i run that aaa.fas example file

file : aaa.fas
>gi|125486661|gb|EL515581.1|EL515581 EST2 Capsicum annuum L. partial CDK library Capsicum annuum cDNA clone 22 5', mRNA sequence
GGATCCCCGTGTTGAAAAACGTTTTTGTATCAAATGCTCCGGGGTATTGCTTATTGTCATTCTCATAGAG
TTCTTCACCGAGATCTGAAGCCTCAGAACTTGCTGATAGATCCACGAAGCAATGTGTTAAAGCTTGCAGA
TTTTGGATTGGGTAGAGCATTTGGTATTCCTGTTAGAACCTTCACTCATGAGGTGGTGACATTATGGTAC
AGGGCACCAGAAATACTGCTTGGATCAAGGCAGTACTCTACTCCGGTTGATGTGTGGTCAGCTGGTTGCA
TATTTGCTGAGATGGTTAACCACCGACCCCTATTTCCTGGTGACTCGGAGATTGATGAACTTTTCAAGAT
TTTCAGAGTGGTGGGTACTCCAAATGAGGATACATGGCCTGGAGTGACTTCTTTGCCTGATTATAAATCT
GCATTTCCAAAATGGCCTCCTAAGGATCTGGCAACTGTAGTCCTGAATCTTGATACGGCAGGACTGGATC
TCCTCGGTAAAATGCTCTCCATGGACCCCGGCAAGAGAATCACCGCCAGGAGTGCCCTTGAACATGAGTA
CTTCAAGGATATCGGCCACTTTCCATGACTCTTGGCATGTCTATCAACAATGCAAACAGAAATTGCTCCG
GTTCTATCTTATGTTCAGTAGCGTTCATGCTCCCTCAAGGACGCACTGAGAGCTC

>Contig1
AAGCTTCTCAACGCTGCAATTGTTGAAATTGCAAGTCTTGTTTATGGCATCAATGACATC
AAGACTCACCATTTCTGTACTATAAAAGGAGCTCATTAGCTCCATGAAAATACACCCAAG
ACAGAGAGAAAAATAATGGAGAGCGGTGAGGTATTTCAGTTTGTGATAAAAAATTAGTCT
GTG

>Contig2
AAGCTTCTCAACGCTGCAATTGTTGAAATTGCAAGTCTTGTTTATGGCATCAATGACATC
AAGACTCACCATTTCTGTACTATAAAAGGAGCTCATTAGCTCCATGAAAATACACCCAAG
ACAGAGAGAAAAATAATGGAGAGCGGTGAGGTATTTCAGTTTGTGATAAAAAATTAGTCT
GTG

.......


i always get just 1 result of head of file (there;s no result of contig1 , contig2 and etc)

why is it happen?

i read many book of ur blast then sequence joined files could get result of every sequences

is there any option wrong?

really need ur help

thx a lot~

It works for me. Within the file aaa.out you should have as many blast results as there are query sequences in aaa.fas. Look for the string "Searching.............." and you will find the results. I did notice that both contig1 and contig2 sequences are the same however, so you have duplicate results for those in the result file.

-Dave