split annotations

[MCH74]

Hi,
It's possible that a few thousand gene annotations have been split into several parts. These neighbouring 'genes' map to non-overlapping regions of the same target protein.
When looking back at the evidence, there were indeed some protein alignments that spanned the whole regions in question that are now annotated as two or three genes. But were not captured by transcripts or AUGUSTUS.
These alternative, longer annotations are not available in the EVM out files. Do you have a suggestion how I can re-annotate the questionable regions without rerunning the entire annotation?
Thank you for your help,
Mark

[brianjohnhaas]

hi, If you have RNA-seq data, you could use a tool like PASA to 'fix' gene models that need to be merged. I don't see a solution based on the protein alignment evidence without needing to revisit the ab initio predictions and training/optimization.

…

On Wed, Mar 24, 2021 at 7:14 AM MCH74 ***@***.***> wrote: Hi, It's possible that a few thousand gene annotations have been split into several parts. These neighbouring 'genes' map to non-overlapping regions of the same target protein. When looking back at the evidence, there were indeed some protein alignments that spanned the whole regions in question that are now annotated as two or three genes. But were not captured by transcripts or AUGUSTUS. These alternative, longer annotations are not available in the EVM out files. Do you have a suggestion how I can re-annotate the questionable regions without rerunning the entire annotation? Thank you for your help, Mark — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3DF2RX442P352YWWLTFHCQZANCNFSM4ZXBHHVA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[MCH74]

Thanks for the tip, Brian. I will consult my pasa output