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Questions tagged [emboss]

Use this tag for questions about the EMBOSS suite of tools. Please also mention your operating system when asking about such tools.

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1 answer
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How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...
2 votes
2 answers
76 views

How can I run the fdnadist command from the EMBOSS package?

My operating system is Mac OS X. I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
1 vote
1 answer
68 views

Using python to call Emboss wordcount

Hi guys I would like to run wordcount from Emboss in a bunch of fasta files. I tried this: ...
2 votes
2 answers
431 views

seqret error when trying to transform GFF3 and FASTA files into EMBL format

I am using the tool seqret from emboss to transform an annotation file in GFF3 format and a FASTA file into an EMBL file because Wormbase does not supply an EMBL file with annotation and sequence ...
1 vote
1 answer
210 views

seqret: Warning: bad /protein_id value

I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence: ...