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:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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blastn analysis shows 98% identity for a gene which is shown to be absent by abricate analysis #119

Closed tanu121093 closed 4 years ago

tanu121093 commented 4 years ago

In individual blastn analysis for genes, I am getting 100% coverage and 98% identity for a gene OXA-51 in strains where abricate analysis summary was showing its absence. Kindly explain this discrepancy in result.

pepijnhuizinga commented 4 years ago

Could you supply a little more information, such as what database did you use in both searches. And in the abricate result, is there another gene called in the same region? (check node and location) that is similar to OXA-51.

tanu121093 commented 4 years ago

i have used ncbi database in both cases. No other gene similar to OXA-51 is present in that strain. The ncbi accession number of gene OXA-51 is same for abricate and blast results.

On 11/22/19 05:48 PM, pepijnhuizinga notifications@github.com wrote:

Could you supply a little more information, such as what database did you use in both searches. And in the abricate result, is there another gene called in the same region? (check node and location) that is similar to OXA-51.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub(https://github.com/tseemann/abricate/issues/119?email_source=notifications&email_token=AMWSLAFQEZPP56M3BCUSI3DQU6VUPA5CNFSM4JQMWR3KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEE5FXPA#issuecomment-557472700), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMWSLAEKBRPQHPI3FVZY333QU6VUPANCNFSM4JQMWR3A).

tseemann commented 4 years ago

@tanu121093 are you sure you used the exact same databases in your "manual analysis" versus using "abricate" ?

Do you monitor the NBCI database change logs? There is a new changelog in every release: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinder/data/ => https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinder/data/latest/changes.txt

HMM Modified:  NF000268.2 blaOXA-51_like updated to NF000268.2 blaOXA-55_like-NCBI
tanu121093 commented 4 years ago

thank you for the reply.

tseemann commented 4 years ago

@tanu121093 you didn't answer any of the questions so I won't be able to help anymore. i hope you resolved the discrepancy.

tanu121093 commented 4 years ago

i have resolved the problem. There is no issue in results provided by abricate software. Actually, the gene i was looking for(oxa-51), has various forms that are showing 98% identity and abricate has included results for 100% identical forms of gene only. Thank you so much for the reply.

On 11/26/19 08:39 AM, Torsten Seemann notifications@github.com wrote:

@tanu121093(https://github.com/tanu121093) you didn't answer any of the questions so I won't be able to help anymore. i hope you resolved the discrepancy.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub(https://github.com/tseemann/abricate/issues/119?email_source=notifications&email_token=AMWSLACBVZRIDOLELKXKNQ3QVSHPBA5CNFSM4JQMWR3KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFERUVY#issuecomment-558438999), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMWSLAEE56OTOEOVUFV3FBDQVSHPBANCNFSM4JQMWR3A).