How to remove internal stop codons from BUSCO identified orthologous genes?

Question

[kabir.deb]

I have implemented BUSCO on few Genomes downloaded from NCBI, and I got multiple internal stop-codons in between the orthologous genes, how to remove or replace them with gaps.

[lieven.sterck]

Can you elaborate why you want to do so?

If the orthologous genes that are being picked up have (in-frame) stopcodons it must mean that the genomic sequence of the species you compare it with is not in great shape. If that is not the case you might be looking at pseudo-genes or such?

Bottom-line: don't simply remove stopcodons without looking into why there are stopcodons present.

[kabir.deb]

Hello,

Actually I want to do phylogenetic analysis and substitution rate (ka/ks) calculation of orthologous gene set of a particular group of species (Gs). After sorting the common orthologous genes of Gs I implemented TranslatorX to align each orthologous genes. But TranslatorX result shows that few of the species have multiple stop codons within the sequence so run aborted.

Just one day before I found a software named macse.jar which can replace internal stop codons. However this software giving an error (

String index out of range: 2996

) after running below code:

$java -jar macse.jar -prog exportAlignment -align EOG090W002U.fna -codonForInternalStop NNN -out_NT New.fasta

[lieven.sterck]

I'm not aware this specific software, sorry.

You could of course bluntly replace the stopcodons with a X in the aminoacid or with Ns in the CDS sequence.