SEA-PHAGES | In Genbank

Link to this post \| posted 04 Sep, 2020 19:25
kmaclea	So I was just browsing and saw our first phage, Yavru, is reported as "In Genbank" and has an accession number. But the number leads nowhere and NCBI these days is horrible to browse and find anything in Genbank (at least in my hands). MT889364: http://www.ncbi.nlm.nih.gov/nuccore/MT889364 Any tips to find the sequence? Want to show the students their names in lights! Kyle= – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 04 Sep, 2020 19:25

So I was just browsing and saw our first phage, Yavru, is reported as "In Genbank" and has an accession number. But the number leads nowhere and NCBI these days is horrible to browse and find anything in Genbank (at least in my hands).

MT889364: http://www.ncbi.nlm.nih.gov/nuccore/MT889364

Any tips to find the sequence? Want to show the students their names in lights!

Kyle=

–
Kyle MacLea
Associate Professor, University of New Hampshire at Manchester
kyle.maclea@unh.edu +1 603-641-4129

Link to this post \| posted 04 Sep, 2020 19:46
debbie	Kyle, It is up to GenBank. They promise an accession number in 3 days when a genome is submitted. Then they have to process it. That time is unpredictable. My last submissions took ~ month. debbie

Link to this post \| posted 04 Sep, 2020 20:04
kmaclea	Thank you, Debbie. I've also noticed they are extremely variable with activation times. It's odd because they create the number so you'd think putting it up would be easy once you have that, but I guess not! Thanks! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post \| posted 12 Jan, 2022 05:30
smarkov	Our last phage Marge already for two months in GenBank but still shows "no items found". Sergei Markov

Link to this post \| posted 12 Jan, 2022 12:15
debbie	Sergei, GenBank has taken as little as 1 day and as much as 6 months to post genomes. I think it is best to just be patient and wait for the genome to post. Are you writing a MRA? debbie

Link to this post \| posted 12 Jan, 2022 22:01
smarkov	Yes, that was my plan for this Winter Break, to write another paper for MRA and include this phage Marge into it. Sergei

Link to this post \| posted 17 Feb, 2022 00:15
hnance@ccga.edu	Can you suggest a format for students to use when referencing or citing their annotation in a CV or resume? Thanks!

Link to this post \| posted 17 Feb, 2022 04:19
smarkov	I am using a format I found on NCBI website: https://support.nlm.nih.gov/knowledgebase/article/KA-03391/en-us For bacteriophage Marge this format is as below: Markov, S.A., Brooks, S.A., Conner, E.M., Gracia-Toro, M., Hale, D.M., Hensley, A., Hohman, E.C., Holland, W.Q., Kelly, C.R., Primasing, W.S., Tucker, L.M., Vogelpohl, J.A., Zimmer, R.J., Tolsma, S., Garlena, R.A., Russell, D.A., Jacobs-Sera, D. and Hatfull, G.F. Mycobacterium phage Marge, complete genome. Accession No. OL549190. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2022. Available from: https://www.ncbi.nlm.nih.gov/nuccore/OL549190 Sergei

Link to this post | posted 17 Feb, 2022 04:19

smarkov

I am using a format I found on NCBI website:
https://support.nlm.nih.gov/knowledgebase/article/KA-03391/en-us

For bacteriophage Marge this format is as below:

Markov, S.A., Brooks, S.A., Conner, E.M., Gracia-Toro, M., Hale, D.M., Hensley, A., Hohman, E.C., Holland, W.Q., Kelly, C.R., Primasing, W.S., Tucker, L.M., Vogelpohl, J.A., Zimmer, R.J., Tolsma, S., Garlena, R.A., Russell, D.A., Jacobs-Sera, D. and Hatfull, G.F. Mycobacterium phage Marge, complete genome. Accession No. OL549190. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2022. Available from: https://www.ncbi.nlm.nih.gov/nuccore/OL549190

Sergei

Link to this post \| posted 18 Feb, 2022 17:30
cdshaffer	I also tell my student to put genbank submissions in a section other than "publications" if they are going to a formal CV since genbank submissions are not really "peer reviewed". I feel like too scientists might object to this as dishonest padding of a CV. I do tell students they should put this on their CV though, as it is important work that deserved recognition (especially for a freshman) so I suggest creating a section called "authored submissions" or "authored contributions". The idea is that we all agree that the work displayed in genbank is important enough that it deserves authorship so it should also be on your CV just don't call it a "publication" and keep that section for authorship on a peer reviewed article (i.e. MRA)

Link to this post | posted 18 Feb, 2022 17:30

cdshaffer

I also tell my student to put genbank submissions in a section other than "publications" if they are going to a formal CV since genbank submissions are not really "peer reviewed". I feel like too scientists might object to this as dishonest padding of a CV. I do tell students they should put this on their CV though, as it is important work that deserved recognition (especially for a freshman) so I suggest creating a section called "authored submissions" or "authored contributions". The idea is that we all agree that the work displayed in genbank is important enough that it deserves authorship so it should also be on your CV just don't call it a "publication" and keep that section for authorship on a peer reviewed article (i.e. MRA)

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