Re: [Artemis-users] Re: Can ACT do a protein comparison?
Title: Re: [Artemis-users] Re: Can ACT do a protein comparison? 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 + 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. >>> >> > > > > ___ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users -- Peter Reeves Phone 61-2-93512536 Professor of Microbiology, School of Molecular and Microbial Biosciences (G08) The University of Sydney NSW 2006, Australia ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Re: Can ACT do a protein comparison?
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. >>> >> > > > > ___ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Re: Can ACT do a protein comparison?
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. >> > ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Can ACT do a protein comparison?
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. > ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
