Identify Translated Sequence in Batch

[pinkrain1010]

Does anyone have any suggestions on how to identify in batch for isoseq data the start and stop positions for predicted gene sequence?

ATGpr web-based software can do this for single genes but not in batch.

Thank you!

[bowhan]

I would use "TransDecoder" and "Trinotate" from the Trinity package.

Trinity was developed to perform de novo transcriptome assembly using illumina data. TransDecoder takes the output fasta file and find coding sequence. You can easily feed into it the output of Iso-Seq pipeline (Quiver polished fasta). Optionally it can also take a GTF file.
PacBio's ANGEL does the same thing.

Trinotate does the annotation by aligning the sequences against known protein databases with BLAST and HMMER.

They are only available on the command line.

[pinkrain1010]

Thank you bowhan, I will look into those. We're actually using Trinity for some analysis with illumina reads from the same samples, but just starting the process so haven't made it through to those steps in the pipeline.