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Trim CDS to ORF
written by jaredbernard 3Does anyone know how to extract CDS from transcripts? I have transcripts structured like this: Xspecies1234-mRNA transcript offset:272 AED:0.06 eAED:0.06 QI:272|1|1|1|0.8|0.83|6|66|318 Notice the `transcript offset` …
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How to add the coordinates of UTRs, CDS, start codon and stop codon to
written by Issac 4Hi there, I have a document in .gff format in which there is a list of coding intergenic transcripts. The basic annotations of each transcript …
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Annotation of vcf with snpEff
written by Peerzada 1Hello Everyone, I have a multi sample vcf file of a particular gene for 1000 individuals . I annotated it with snpeFF. I want to …
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Why is an effective length of a trasncript better than normal length?
written by Lucie 0Hello, I would like to ask, why is the effective length of transcript (which is used in for example RSEM or Salmon) better than normal …
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Lengths of UTR3, UTR5 and ORF from gtf file
written by bio_elle 1I would like to find the lengths of UTR3, UTR5 and ORF regions for each transcript of protein coding genes. My plan was to find …
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Variant splicing position on CDS
written by heureuse 1Hello, I would like to know how I can find the position of a variant splicing on coding sequence. I'm using Aloft but if there …
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Removing all stop codons from Sequence Record using Biopython
written by ckan91 4Hello Everyone, I have sequences that occasionally have an erronious stop codon. Is there a way to filter a biopython Sequence Record of all stop …
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How to extract start codon and stop codon from a fasta of multiple protein coding genes !
written by kabir.deb 9I want to know that is there is any suitable tool for extracting start codon and stop codon from the fasta file of multiple protein-coding …
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Where to get Gene start position to end positon for all gene in an organism
written by Bioblazer 5In a transcript file (.gtf) we can able to get exon wise start position and stop position, CDS and start codon region and stop codon …
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Protein variant notation for an inserted stop codon?
written by alex.rubinsteyn 19How do I annotate the protein effect of an in-frame insertion of a "TAG" stop codon inside a cDNA sequence? Typically, I would annotate an …