Hello,
I'm student in bioinformatics and I'm currently undergoing training at INRA
Toulouse (France) under the supervision of Helene Chiapello and Christine
Gaspin.
I have a question about the Mauve software concerning the "extract
ortholog" feature provided by the GUI. Indeed, I have encountered several
problems while analyzing a large dataset of 27 E. coli genomes: for several
ortholog groups, I identified multiple overlapping coding sequences in the
same genome.
After manual inspection, I realize that these overlapping CDS seem mainly
enlight two situations :
=> Annotation mistakes in the original genbank file: overlaping coding
sequences are located at different reading frames in the same genomic
region. In this case, I was able to choose one of the two coding sequences
by looking at %identity and coverage of the alignments.
=> Real overlapping coding sequences: strongly annotated and predicted CDS,
located at same reading frame (with a coding sequence included in another
one for example). It should also be possible here to choose the real
otholog CDS among the two coding sequences by looking at alignment
coverage.I'd like to know if a fix already exists to handle these cases. Or
may be you plan to do it ? Last question : is there a way to extract
orthologs using a command-line program ?
Thank you in advance for you answer.
Best regards,
Franck Cerutti.
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