Questions about protein data support

[Tang-pro]

Hi, @brianjohnhaas

RNAsamba is a software that can predict protein sequences based on transcripts, but there is no cds sequence here. So here I use the protein sequence predicted by Rnasamba as the blastp database. Is this method feasible?

[brianjohnhaas]

Yes, that should work.

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On Sat, Mar 16, 2024 at 6:32 AM Tang JIWEI ***@***.***> wrote: Hi, @brianjohnhaas <https://github.com/brianjohnhaas> RNAsamba is a software that can predict protein sequences based on transcripts, but there is no cds sequence here. So here I use the protein sequence predicted by Rnasamba as the blastp database. Is this method feasible? — Reply to this email directly, view it on GitHub <#198>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXY3LOHYHUXLMDNUFJ3YYQNVDAVCNFSM6AAAAABEZGZ7L2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DSOJQGI4TOOA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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

[brianjohnhaas]

Note, you could combine that with search results to other protein databases if you want.

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On Sat, Mar 16, 2024 at 8:43 AM Brian Haas ***@***.***> wrote: Yes, that should work. On Sat, Mar 16, 2024 at 6:32 AM Tang JIWEI ***@***.***> wrote: > Hi, @brianjohnhaas <https://github.com/brianjohnhaas> > > RNAsamba is a software that can predict protein sequences based on > transcripts, but there is no cds sequence here. So here I use the protein > sequence predicted by Rnasamba as the blastp database. Is this method > feasible? > > — > Reply to this email directly, view it on GitHub > <#198>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABZRKXY3LOHYHUXLMDNUFJ3YYQNVDAVCNFSM6AAAAABEZGZ7L2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DSOJQGI4TOOA> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

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

[Tang-pro]

Hello, @brianjohnhaas
Thank you for your reply！
However, through this method, the original protein sequences predicted by RNAsamba were 174,084, but the cds sequences obtained through TransDecoder were only 171,513. How should we understand this? Is it feasible?

[brianjohnhaas]

Not sure - maybe it has to do with the length of the cds sequence.

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On Sat, Mar 16, 2024 at 9:34 AM Tang JIWEI ***@***.***> wrote: Hello, @brianjohnhaas <https://github.com/brianjohnhaas> Thank you for your reply！ However, through this method, the original protein sequences predicted by RNAsamba were 174,084, but the cds sequences obtained through TransDecoder were only 171,513. How should we understand this? Is it feasible? — Reply to this email directly, view it on GitHub <#198 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX55B6UZQD35O7BZ4DDYYRC75AVCNFSM6AAAAABEZGZ7L2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBRHE4DQOBSGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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

[Tang-pro]

Hi, @brianjohnhaas

Thank you for your reply!
Best！

[Tang-pro]

Hi, @brianjohnhaas

ORF type:internal Should this type of cds sequence be retained?
Based on the above method, does the type of Internal in the obtained cds sequence need to be eliminated? However, this corresponding ID is the predicted protein sequence in Rnasamba, so how to deal with this situation?

[brianjohnhaas]

If the transcript is partial, that's the best it can do.

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On Wed, Mar 20, 2024 at 6:57 AM Tang JIWEI ***@***.***> wrote: Hi, @brianjohnhaas <https://github.com/brianjohnhaas> ORF type:internal Should this type of cds sequence be retained? — Reply to this email directly, view it on GitHub <#198 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZRVW4COOJA2Y25USDYZFTRPAVCNFSM6AAAAABEZGZ7L2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGI4DOMRYG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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

[Tang-pro]

@brianjohnhaas
Does it mean to eliminate 5prime_partial and 3prime_partial?

[brianjohnhaas]

no, it means that it's both 5' partial and 3' partial, so missing start and stop codons. The entire transcript translates from beginning to end and so presumably the more central part of the coding region.

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On Wed, Mar 20, 2024 at 9:12 AM Tang JIWEI ***@***.***> wrote: @brianjohnhaas <https://github.com/brianjohnhaas> Does it mean to eliminate 5prime_partial and 3prime_partial? — Reply to this email directly, view it on GitHub <#198 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3HJ5ZJ3TLVVYCWTF3YZGDNDAVCNFSM6AAAAABEZGZ7L2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGUZTOOBXGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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

[Tang-pro]

@brianjohnhaas

So I don't quite understand what should be the situation of culling transcripts?