So any command line option to grep the information from NCBI Taxonomy ?
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virus classification
I have a lots of data about species of viruses and I want to know about the family information of those viruses. I have downloaded the ICTV classification table of 2020. Still I am not able the get the information about the family information of those virus species.
Streptococcus virus EJ-1 #N/A
Lactobacillus virus Lc-Nu #N/A
Lactobacillus virus phiAT3 Siphoviridae
Streptococcus virus O1205 Siphoviridae
Mycobacterium virus Pacc40 Siphoviridae
Sinorhizobium virus PBC5 #N/A
Abelson murine leukemia virus #N/A
Salmonella virus SETP3 Siphoviridae
Clostridium virus phiC2 #N/A
Enterobacteria virus N4 #N/A
Invertebrate iridescent virus 3 Iridoviridae
Staphylococcus virus Twort Herelleviridae
Bacillus virus SPO1 Herelleviridae
Vibrio virus VHML Myoviridae
Streptococcus virus DT1 Siphoviridae
Yersinia virus L-413C #N/A
Chlamydia virus CPAR39 Microviridae
Bacillus virus B103 Salasmaviridae
Streptococcus virus PH10 #N/A
Prochlorococcus virus P-SSM2 #N/A
Lactococcus virus TP901-1 #N/A
Streptococcus virus phi3396 #N/A
Flavobacterium virus 11b #N/A
Streptococcus virus 5093 #N/A
Staphylococcus virus phiSauS-IPLA35 #N/A
Like this I am getting . Can anyone please help me out .
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2 answers
Just because some names are not found in the NCBI taxonomy database due to naming inconsistency, e.g. Streptococcus phage EJ-1 is in, but Streptococcus virus EJ-1 is not.
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shenwei356
Taxonomic information in ICTV is manually curated and thus it usually lags behind virus data from NCBI. There are many virus species in NCBI that have not yet been covered by ICTV.
As shenwei365 suggested, you can get taxonomic information of your viruses from NCBI Taxonomy.
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Andrzej Zielezinski
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