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Forum: Bioinformatics 05-03-2015, 10:24 AM
Replies: 1
Views: 2,322
Posted By atape
Question: Is it possible to get local blast output directly in Biopython, without mak

Hi

I am currently filtering through a large amount of reads from a 454 machine. I would like to blast every read against a local blast database and check if the sequence is indeed from a targeted...
Forum: Bioinformatics 01-31-2015, 01:55 PM
Replies: 0
Views: 1,641
Posted By atape
Abnormal reading of FASTA file by PAL2NAL

I am making a script that produces as an output a protein alignment in fasta format and an appropriate mRNA fasta file for latter use with the PAL2NAL algorithm that gives a codon aware alignment.
...
Forum: Bioinformatics 07-10-2014, 09:00 AM
Replies: 0
Views: 987
Posted By atape
Mapping matrix presance/absance on a phylogenetic tree?

Do you know of any algorithms that would allow me to map absence and presence of a certain state onto a user generated phylogenetic tree? Thanks!

Example:

000110010101?001010001100011010010...
Forum: Bioinformatics 05-10-2014, 12:39 AM
Replies: 1
Views: 1,532
Posted By atape
Codon alignment

I need to make an alignment based of codons, for determining dN/dS ratio in PAML.

What is a good and reliable way of making it, by using both nucleotide and aa sequences for the alignment?

For...
Forum: Bioinformatics 01-25-2014, 02:05 AM
Replies: 0
Views: 1,548
Posted By atape
Converting EST2genome file format to BED file format?

Is there any easy (automated) way to convert the data output from EST2genome to BED format? Thank you
Forum: Bioinformatics 07-05-2013, 03:11 AM
Replies: 8
Views: 4,141
Posted By atape
Thanks guys and gals :) Exonerate is...

Thanks guys and gals :)

Exonerate is working out nicely, but will try all the algorithms that have been listed, just to see which gives the most favourable results.

One more thing though,...
Forum: Bioinformatics 07-03-2013, 05:39 AM
Replies: 8
Views: 4,141
Posted By atape
Software for aligning cDNA onto reference genomic sequences to retrieve INTRONS

Hi,

which software would you recommend for the task? I need to retrieve introns from genomic sequences by aligning cDNAs on to them.

Thank you :)
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