User: jan

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jan0
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Posts by jan

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Merging of sequence chunks
... Thanks JC, the script is doing the job! ...
written 2 days ago by jan0
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Comment: C: Merging of sequence chunks
... Sorry, my fault. After running sudo apt install default-jdk, it worked. The tool is just great! Thank you very much :-) Could the script also be modified in a way that it accepts headers that are identical only before the "@" sign (e.g., >red@abcd and >red@efgh)? ...
written 3 days ago by jan0
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Comment: C: Merging of sequence chunks
... Thanks Pierre! Unfortunately, however, I don't seem to be able to install BioAlcidaejdk (there is no bioalcidaejdk.jar in dist/). Can you maybe provide some guidelines how to install this? Is it also running on a Mac? ...
written 3 days ago by jan0
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Merging of sequence chunks
... Hello! I would like to merge all amino acid sequences with identical names in a given fasta file (trimmed alignment). I know that this can be done for manually selected sequences with Aliview, however, I am looking for a tool or script (bash, perl, python) that allows me to do that for hundreds of ...
alignment sequence written 3 days ago by jan0
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Comment: C: How to remove sequences from a fasta file based on ID list?
... Thank you! This works well on Linux (couldn't make it run on OSX before and therefore hoped to find a raw/executable script here). ...
written 7 months ago by jan0
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Comment: C: How to remove sequences from a fasta file based on ID list?
... I found a similar question asked by the users Ginsea Chen and Seta. If you check the answers, however, you will see that it has been shown how to remove sequences based on provided short sequences that are matching or to remove sequences with a given pattern in the IDs/header. There are also answers ...
written 8 months ago by jan0
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(Closed) How to remove sequences from a fasta file based on ID list?
... Hi all, I am looking for a way that allows me to filter out (remove) some sequences from a fasta file (with aligned protein sequences) based on a list of headers given as separate input file. I am aware that there are similar questions here but in most cases, the given answers show how to get and no ...
sequence alignment written 8 months ago by jan0
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Comment: C: Add sequence lengths to headers in a fasta file
... Great, that's exactly what I was looking for. Thank you! ...
written 9 months ago by jan0
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Add sequence lengths to headers in a fasta file
... Hi all. I have a fasta file and would like to add the sequence lengths to the headers by **keeping** the sequences. Thank you! My file: >Seq_1 MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGI KILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAA KGTVGSILDRKDET ...
sequence written 9 months ago by jan0 • updated 9 months ago by WouterDeCoster24k

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