SEA-PHAGES | All posts created by aajohnson

Link to this post \| posted 22 Feb, 2023 20:25
aajohnson	This was useful today! Thank you.

Posted in: Cluster EC Annotation Tips → Tail Assembly Chaperone in KaiHaiDragon

Link to this post \| posted 22 Feb, 2023 20:00
aajohnson	debbie Hi Kyle, So if you continue to investigate, there is no supporting data for a minor tail protein except NCBI said so. there is no way that a functional call can be made from the blast data that HHPred data sources does not support." We're getting no blastp CDD or HHPred support for at least two "minor tail proteins" in cluster K phages, including in the publication supplementary tables posted there. I would call them as hypothetical protein. I haven't dug yet for any synteny rules or something related to these- can you point me towards something to use? I commiserate with you Kyle.

Link to this post | posted 22 Feb, 2023 20:00

aajohnson

debbie
Hi Kyle,
So if you continue to investigate, there is no supporting data for a minor tail protein except NCBI said so. there is no way that a functional call can be made from the blast data that HHPred data sources does not support."

We're getting no blastp CDD or HHPred support for at least two "minor tail proteins" in cluster K phages, including in the publication supplementary tables posted there. I would call them as hypothetical protein. I haven't dug yet for any synteny rules or something related to these- can you point me towards something to use?
I commiserate with you Kyle.

Posted in: Functional Annotation → RefSeq and INSDC name disagreements in NCBI Blast for Functonal Assignment

Link to this post \| posted 04 Feb, 2016 18:52
aajohnson	I'm definitely interested. My student work on laptops, and we create a Windows VM for the students with Macs to run DNA Master but it's a hassle for a variety of reasons. I'd love it they only had one install. Edited 04 Feb, 2016 18:52

Posted in: DNA Master → Running DNA Master on the Ubuntu SEA Virtual Machine

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