On using BLASTX to find the protein coding frame
Hello All,
I'm using BLASTX to find the correct frame that contains the protein coding region fin the cDNA of a eukaryotic species. Because the sequence contain frameshifts, I'm getting multiple hits from different frames.
The hit details are as follows:
So, which frame to choose? And how to get the protein sequence once the correct frame is determined ? Can I run EMBOSS Transeq , to translate the chosen frame? Does some other way of merging the different hsps from the same frame exist?
p.s. For this particular case ESTSCAN with default params. failed to generate any peptide sequence.
I'm using BLASTX to find the correct frame that contains the protein coding region fin the cDNA of a eukaryotic species. Because the sequence contain frameshifts, I'm getting multiple hits from different frames.
The hit details are as follows:
So, which frame to choose? And how to get the protein sequence once the correct frame is determined ? Can I run EMBOSS Transeq , to translate the chosen frame? Does some other way of merging the different hsps from the same frame exist?
p.s. For this particular case ESTSCAN with default params. failed to generate any peptide sequence.
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