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Forum: Bioinformatics 08-02-2017, 07:39 AM
Replies: 1
Views: 610
Posted By ac91
Extract sequence with largest size

Hi,

I need to extract the sequence with the largest size of multiple fasta files (the sequence with the longest length, excluding gaps). Can anyone help me?

Thanks!
Forum: Bioinformatics 07-03-2017, 01:37 AM
Replies: 6
Views: 1,757
Posted By ac91
Sorry for the late reply. You can find my...

Sorry for the late reply.
You can find my files attached, but I changed the fasta and phylip to .txt because is impossible to attach files with that extensions.
Forum: Bioinformatics 06-30-2017, 01:13 AM
Replies: 6
Views: 1,757
Posted By ac91
Sorry Brian, but seems that your script does not...

Sorry Brian, but seems that your script does not work well with my files. Can you tell me why?

For example:
file.phy
3 120
seq1 ATGTGTTCAGCTCTAGTCGACAAGTATTTCAACTACCAGGAACCTCCGAATCGACAACTT...
Forum: Bioinformatics 06-29-2017, 10:54 AM
Replies: 6
Views: 1,757
Posted By ac91
Thanks so much! I already saw that there are...

Thanks so much!

I already saw that there are others useful scripts in bbmap.
Forum: Bioinformatics 06-29-2017, 07:01 AM
Replies: 6
Views: 1,757
Posted By ac91
phylip to fasta

Hi,

Can anyone provide me a script in python or perl that converts phylip interleaved into fasta? I already found some scripts but it seems that they all work with phylip sequential and not...
Forum: Bioinformatics 06-16-2017, 05:36 AM
Replies: 1
Views: 517
Posted By ac91
Biomart - export the highest transcript

Hi,

Does anyone know if it is possible to export a specific transcript from biomart? I just want to export the highest one.

Thanks!
Forum: Bioinformatics 05-30-2017, 07:11 AM
Replies: 3
Views: 843
Posted By ac91
Thanks for the reply! Im using...

Thanks for the reply!

Im using -max_target_seqs 100 but I have more than 100 hits per query.
I believe that max_target_seqs doesn't specify the maximum number of hits per query, but the maximum...
Forum: Bioinformatics 05-30-2017, 03:17 AM
Replies: 3
Views: 843
Posted By ac91
Blastx_Nhits and MinIdentity

Hi,

Im running blastx but I dont known how to get only results for 100 best hits per query and a minimum of 50% of identity. What are the options that allows me to do that?

thanks!
Forum: Bioinformatics 05-31-2016, 05:22 AM
Replies: 0
Views: 704
Posted By ac91
GUIDANCE (software) / BioPerl - help

Hi,

Im running GUIDANCE for some alignments (datatype = codon) and I have some NNN in the middle of the sequences. The software seems to assume these NNN as stop codons.
NOTE: GUIDANCE uses...
Forum: Bioinformatics 08-23-2015, 12:34 PM
Replies: 4
Views: 2,698
Posted By ac91
Thank you very much!!! :)

Thank you very much!!! :)
Forum: Bioinformatics 08-23-2015, 05:11 AM
Replies: 4
Views: 2,698
Posted By ac91
First of all, thanks for your fast answer. I...

First of all, thanks for your fast answer.

I had the idea that e-values were the main criteria to "eliminate" some hits. Im wrong?

Yes, I have some basic knowledge in python programing.
Forum: Bioinformatics 08-23-2015, 03:02 AM
Replies: 4
Views: 2,698
Posted By ac91
Reciprocal blast (RBH) - help

Hi!

Im new in the bioinformatic world so be patience if my question is dummy. :)

I have two fasta files and I run blast reciprocal best hits (RBH) for blastp using the script from peterjc...
Forum: Introductions 08-23-2015, 02:46 AM
Replies: 0
Views: 704
Posted By ac91
Hello

Greetings everybody!!
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