By using Augustus gene predictor i have predicted the genes from draft genome but, how should i confirm that these proteins were full length or incomplete? is there any bioinformatics approach to make the predicted protein sequence as full length sequence by using de-novo sequenced draft genome or from transcriptome data ?
Dear Yogesh, all you need is Blast. Take your sequences and compare them with well annotated sequences of closer model organism and consider the query coverage for any conclusion made be comparisons.
Yogesh, normally the gene-finder programs will tell you if the found gene sequence is complete or partial. This is quite easy to recognize in prokaryotic data because of the simple check of presence of the STOP codon. In eukaryotic data this can be more tricky because the start and end of introns/exons is not always the same. However, if you train your gene-finder with a properly close sequence genome this can also be done with considerable effectiveness. So, if the software you mention does not give this information, I would recommend you to use another software package and do a proper training with a close genome sequence.
Then, you can use BLAST as already suggested against an appropriate genome and by examining the alignment you can tell/confirm if your sequence is partial or complete, relative to the genome you are using to compare.
Best regards,
---sram
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools