SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

Recent Activity

Viknesh Sivanathan posted in Recording Data for Attempts to Raise Lysogens

mcclory posted in Webbed plate hack for low-titer stocks and small plaques

nic.vega posted in Covaris fragmentation

Tamarah Adair posted in MRA required information

Dan Russell posted in MRA required information

All posts created by Schaudhary

| posted 04 Apr, 2022 03:39
default avatar
Schaudhary
debbie
Hi Shima,
Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total.
It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different.
debbie

Hello Debbie, thank you for the clarification. We will keep the stop codon of ORF to compare the gene.
Posted in: Gene or not a Gene → Phage DB and DNA Master number of genes mismatch
| posted 31 Mar, 2022 20:34
default avatar
Schaudhary
Hello, we want some help as to how to go about with the number of genes not matching in DNA Master after auto-annotation and Phage DB. The DNA Master report 74 and Phage DB reports 72 genes. Gene 1 in PECAAN is forward where as in the Phage db and DNA Master is reverse. Any advice…
Posted in: Gene or not a Gene → Phage DB and DNA Master number of genes mismatch
| posted 12 Mar, 2022 02:15
default avatar
Schaudhary
debbie
Amanda,
HI! Sorry for the delay in my response too!
Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output.
Use the cover sheet to describe what you have done and all should work out.
debbie

Hello Debbie,
I have a question, by PECAAN output do we mean the notes part as when we do the output the synteny notes written separately do not show up. Can we add it separately to the output notes? We are exporting the new SEA Format in PECAAN.
Edited 12 Mar, 2022 02:16
Posted in: Notes and Final Files → Question about notes template
| posted 12 Mar, 2022 02:15
default avatar
Schaudhary
debbie
Amanda,
HI! Sorry for the delay in my response too!
Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output.
Use the cover sheet to describe what you have done and all should work out.
debbie

Hello Debbie,
I have a question, by PECAAN output do we mean the notes part as when we do the output the synteny notes written separately do not show up. Can we add it separately to the output notes. We are exporting the new SEA Format in PECAAN.
Posted in: Notes and Final Files → Question about notes template