So for tblastx you can just change the program name option and use something like this:
blastall -d Seq1_fasta -i Seq2_fasta -p tblastx -m 8 -o $outputfile
Regards
Tim
On 7/11/06 23:30, "Peter Reeves" <[EMAIL PROTECTED]> wrote:
Dear Tim,
I was about to try tBLASTx .
could you tell me the command lines to use.
what I use for current script using dna for the blast is:
seqret -auto -filter -osf fasta $sequence_1 > Seq1_fasta
seqret -auto -filter -osf fasta $sequence_2 > Seq2_fasta
formatdb -i Seq1_fasta -p f
blastall -d Seq1_fasta -i Seq2_fasta -p blastn -m 8 -o $outputfile
where the input files $sequence_1 & $sequence_2 are genbank file or genbank/embl generated by artemis Regards
Peter
At 2:04 PM +0000 7/11/06, Tim Carver wrote:
I should add that you can of course use tBLASTx to generate the comarison
data.
Regards
Tim
On 7/11/06 13:41, "Tim Carver" <[EMAIL PROTECTED]> wrote:
> Hi Bala
>
> No, this is only for DNA sequence comparisons.
>
> Regards
> Tim
>
>
> On 7/11/06 12:02, "BALASUBRAMANIAN GANESAN" <[EMAIL PROTECTED]> wrote:
>
>> Dear Tim/Julian/users
>> Is it also possible to use protein sequence comparisons using this same
>> approach?
>> Regards
>> BALA.
>>> ===== Original Message From Julian Parkhill <[EMAIL PROTECTED]> =====
>>> Bala,
>>>
>>> ACT cannot reconstruct the positional information for the separate
>>> sequences within a multiple FASTA file; BLAST reports only the local
>>> coordinates for the matches. What you need to do is:
>>>
>>> 1) Concatenate all the mFASTA sequences into a single sequence for
>>> each genome (you can do this from Artemis, using the "Write; all
>>> bases" menu)
>>>
>>> 2) Do the blast comparison with the concatenated sequences
>>>
>>> 3) Load the original multiple FASTA files into ACT, but use the
>>> comparison file from the concatenated sequences. You should see the
>>> contigs represented by alternating dark/light brown features, plus
>>> the matches for the whole sequences.
>>>
>>> For the other problem; the set cutoffs only remain for as long as the
>>> dialog window is open. Closing the dialog window resets the cutoffs.
>>>
>>> yours,
>>>
>>> Julian.
>>>
>>
>
>
>
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