Questions tagged [multi-fasta]

Concerning fasta files with multiple sequences in one file

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4 votes
2 answers
313 views

Keeping DNA sequence after changing FASTA header on command line

I have a FASTA header that looks like this: ...
rimo's user avatar
  • 923
1 vote
1 answer
47 views

how to search and calculate occurence of certain word (like TAA) in fastafile

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tonu's user avatar
  • 11
1 vote
1 answer
214 views

Primer trimming-fasta files

My goal: I want to trim off the primers (Forward : CGAGAAGACCCTRTGRAGCT, Reverse : GTTGGGGYGACCNYGG) from a fasta file with a lot of dna sequences allowing for some (e.g. 3) mismatches (identity). ...
Damianos's user avatar
4 votes
1 answer
47 views

Trim reads 1kb upstream of sequence

I need a quick way to trim multiple reads in a FASTA file. I need to trim everything that is 1kbp upstream of this sequence ...
rimo's user avatar
  • 923
4 votes
2 answers
192 views

Searching motifs in sequence and their frequencies

This is a two part question. I am searching for a motif, and in that search I wanted to also find the total number of sequences in my FASTA file, but the code I wrote is not yielding that please see ...
thole's user avatar
  • 143
2 votes
2 answers
35 views

finding overlapping motifs to increase length of motif

I am able to find matching motif in my sequence, and I would like to now find overlapping motifs. Basically, after matching my motif, I want to find the 6 amino acids after it. This is the code below ...
thole's user avatar
  • 143
2 votes
2 answers
242 views

motif searching in a multi-fasta file

I am having trouble trying to search for motifs in a multi fasta file. I have used two techniques one gives me the name of the sequence where the motif is found but doesn't give me the the motif and ...
thole's user avatar
  • 143
2 votes
1 answer
168 views

finding motifs in fasta file with multiple sequences

I am able to find matching motifs on a single sequence, as well as their position as shown below : ...
thole's user avatar
  • 143
2 votes
1 answer
164 views

Add file name to FASTA file header using SeqIO

I have several fasta files that represent the proteins from different orthogroups. However, the orthogroup that each of the proteins belongs to is not indicated within the files. I am leveraging ...
Eduardo Menotti's user avatar
1 vote
1 answer
35 views

Multifasta protein alignment

I have around 4000 orthologous proteins for each of 5 species, I'd like to align them and to concatenate alignments. Which tools can I use? And how? Marco
Marco's user avatar
  • 161
3 votes
3 answers
962 views

How to get strain names/ids contained in a multi FASTA file using seqkit?

FASTA files can be very big and unwieldy, especially if lines are at most 80 characters, one can't speed up browsing them by using less with ...
Cornelius Roemer's user avatar