fasta Questions
4
Solved
QIIME requests this (here) regarding the fasta files it receives as input:
The file is a FASTA file, with sequences in the single line format. That is, sequences are not broken up into multiple li...
Cheryllches asked 11/6, 2014 at 7:1
4
Solved
I would like to extract sequences from the multifasta file that match the IDs given by separate list of IDs.
FASTA file seq.fasta:
>7P58X:01332:11636
TTCAGCAAGCCGAGTCCTGCGTCGTTACTTCGCTT
CAAGTC...
Kalin asked 9/4, 2018 at 11:1
5
Solved
I have a small fasta file of DNA sequences which looks like this:
>NM_000016 700 200 234
ACATATTGGAGGCCGAAACAATGAGGCGTGATCAACTCAGTATATCAC
>NM_000775 700 124 236
CTAACCTCTCCCAGTGTGGAACCTCTAT...
Glossectomy asked 21/1, 2014 at 16:23
2
Solved
I am running ipcress for in silico PCR and the results look like this:
Ipcress result
Experiment: Primer1
Primers: B A
Target: QLOD02000001.1:filter(unmasked), whole genome shotgun sequence
Matches...
4
Solved
I have a table like this:
>head(X)
column1 column2
sequence1 ATCGATCGATCG
sequence2 GCCATGCCATTG
I need an output in a fasta file, looking like this:
sequence1
ATCGATCGATCG
sequence2
GCCAT...
14
Solved
I have a data in that always comes in block of four
in the following format (called FASTQ):
@SRR018006.2016 GA2:6:1:20:650 length=36
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
+SRR018006.2016 GA2:6:1:20...
Raddle asked 9/10, 2009 at 7:22
5
Solved
I often need to find a particular sequence in a fasta file and print it. For those who don't know, fasta is a text file format for biological sequences (DNA, proteins, etc.). It's pretty simple, yo...
3
Is there a way to use BioPython to convert FASTA files to a Genbank format? There are many answers on how to convert from Genbank to FASTA, but not the other way around.
4
I'm trying to read a FASTA file and then find specific motif(string) and print out the sequence and number of times it occurs. A FASTA file is just series of sequences(strings) that starts with a h...
4
Solved
I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe ...
Mitchiner asked 24/11, 2009 at 10:55
9
Solved
I have a fasta file where the sequences are broken up with newlines. I'd like to remove the newlines. Here's an example of my file:
>accession1
ATGGCCCATG
GGATCCTAGC
>accession2
GATATCCATG
A...
Arianna asked 6/4, 2013 at 23:14
4
When I use write.fasta in seqinr, the file that it outputs looks like this:
>Sequence name 1
>Sequence name 2
>Sequence name 3
...etc
Sequence 1 Sequence 2 Sequence 3 ...etc
In other...
3
Solved
I have the following FASTA file:
>header1
CGCTCTCTCCATCTCTCTACCCTCTCCCTCTCTCTCGGATAGCTAGCTCTTCTTCCTCCT
TCCTCCGTTTGGATCAGACGAGAGGGTATGTAGTGGTGCACCACGAGTTGGTGAAGC
>header2
GGT
>header3
TTAT...
1
Solved
Last week I decided to give a try to Perl6 and started to reimplement one of my program.
I have to say, Perl6 is so the easy for object programming, an aspect very painfull to me in Perl5.
My pr...
Claytor asked 24/8, 2018 at 13:3
4
Suppose my long sequence looks like:
5’-AGGGTTTCCC**TGACCT**TCACTGC**AGGTCA**TGCA-3
The two italics subsequences (here within the two stars) in this long sequence are together called as inverte...
3
In short:
how to convert from fasta to "phylip"-like format (without the sequence and residu counts at the top of the file) using sed ?
A fasta format is like this:
>sequence1
AATCG
GG-AT
>...
2
Solved
I want to replace all the headers (starting with >) with >{filename}, of all *.fasta files inside my directory AND concatenate them afterwards
content of my directory
speciesA.fasta
species...
3
Solved
I have an input_file.fa file like this (FASTA format):
> header1 description
data data
data
>header2 description
more data
data
data
I want to read in the file one chunk at a time, so that...
Drum asked 29/7, 2016 at 9:25
2
Solved
I have a 2 files. One is a fasta file contain multiple fasta sequences, while another file includes the names of candidate sequences I want to search (file Example below).
seq.fasta
>Clone_18
...
2
Solved
import gzip
import io
from Bio import SeqIO
infile = "myinfile.fastq.gz"
fileout = open("myoutfile.fastq", "w+")
with io.TextIOWrapper(gzip.open(infile, "r")) as f:
line = f.read()
fileout.write(...
0
I have two files
File 1
chr1:4847593-4847993
TGCCGGAGGGGTTTCGATGGAACTCGTAGCA
File 2
Pbsn|X|75083240|75098962|
TTTACTACTTAGTAACACAGTAAGCTAAACAACCAGTGCCATGGTAGGCTTGAGTCAGCT
CTTTCAGGTTCATG...
Duleba asked 29/4, 2016 at 5:26
4
Solved
I am trying to parse a large fasta file and I am encountering out of memory errors. Some suggestions to improve the data handling would be appreciated. Currently the program correctly prints out th...
2
Solved
I have a FASTA file that can easily be parsed by SeqIO.parse.
I am interested in extracting sequence ID's and sequence lengths. I used these lines to do it, but I feel it's waaaay too heavy (two i...
4
Solved
The description of the problem I am having is a bit complicated, and I will err on the side of providing more complete information. For the impatient, here is the briefest way I can summarize it:
...
Succinct asked 26/1, 2011 at 3:55
2
Solved
Ok so I need to extract part of a sequence from a FASTA file, using python (biopython, http://biopython.org/DIST/docs/tutorial/Tutorial.html)
I need to get the first 10 bases from each sequence a...
Nudd asked 30/10, 2012 at 3:29
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