User: Juke-34
Juke-34 • 2.6k
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Posts by Juke-34
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... They do the same at EBI, they translate the alternative initiation codons as M. ...
written 12 hours ago by
Juke-34 • 2.6k
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... I'm not sure it is what you want but I have a perl script to extract CDS properly (concatenate them). Is is called `gff3_sp_extract_sequences.pl` and you can find in the [GAAS][1] repository.
> gff3_sp_extract_sequences.pl --fasta genome.fa --gff annotation.gff -o cds.fa
It extracts CDS per def ...
written 3 days ago by
Juke-34 • 2.6k
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... It’s pity to drop funannotate after having spent so much energy. There is no way to fix your problem? Maker has also lot of dependencies... if you have installed it give it a try. There are plenty of documentation less verbose made by users on internet.
If you are looking for other annoation tools ...
written 5 days ago by
Juke-34 • 2.6k
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... You would like to update an existing structural annotation based on this new data? Or you want an annotation based only on this trinity data?
You can use PASA Indeed, GAWN or MAKER.
What is your problem with PASA? You have to provide the trinity fasta file, the genome and a list of alignment tool t ...
written 5 days ago by
Juke-34 • 2.6k
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... Do you mean you look for a way to find gene functions?
The common way to go is to run [Interproscan][1]. In one go you reach more than 20 different DB.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142/ ...
written 7 days ago by
Juke-34 • 2.6k
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... I use `gff3_sp_extract_sequences.pl` from the [GAAS][1] repository.
> gff3_sp_extract_sequences.pl --cdna --gff input.gtf --fasta genome.fa -o output.fa
[1]: https://github.com/NBISweden/GAAS ...
written 9 days ago by
Juke-34 • 2.6k
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... I have a perl script for that purpose called `gff3_sp_add_start_and_stop.pl`
> gff3_sp_add_start_and_stop.pl --gff infile.gff --fasta infile.fasta -o
> output.gff
You can specify the codon table to use (1 by default). It deals with start or stop codon that would be split over several exons.
...
written 10 days ago by
Juke-34 • 2.6k
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... 2 Bioinformatician positions
Location: Lund, Sweden
Type of employment: Permanent position
Last application date 05.Sep.2019
https://lu.varbi.com/en/what:job/jobID:279454 ...
written 14 days ago by
Juke-34 • 2.6k
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... Bioinformatican – with focus on Data Steward
Location: Uppsala, Sweden
Type of employment: Permanent position
Deadline 10 September. [https://www.uu.se/en/about-uu/join-us/details/?positionId=277048][1]
[1]: https://www.uu.se/en/about-uu/join-us/details/?positionId=277048 ...
written 14 days ago by
Juke-34 • 2.6k
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... You should maybe consider another approach.
Have a look here [enter link description here][1] table 5.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745/ ...
written 14 days ago by
Juke-34 • 2.6k
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27 days ago,
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For A: Trinity strand specific: RF or FR
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For Bioinformatician in genome annotation, Uppsala, Sweden
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: How to convert exon genomic coordinates to protein coordinates
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For Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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11 months ago,
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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11 months ago,
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For A: Status of maker annotation
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11 months ago,
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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12 months ago,
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For Bioinformatician in genome annotation, Uppsala, Sweden
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For A: How to convert exon genomic coordinates to protein coordinates
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For Bioinformatician in genome annotation, Uppsala, Sweden
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