please help me retrieve these sequences
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7.4 years ago
ashish ▴ 680

I am trying to find orthologues using wheat protein sequences and so I did Blast on phytozome against three different genomes. in results i got the ids of hits. now i want to retrieve sequences using these ids but i am unable to do so. I've tried batch entrez and biomart. if i search these ids indivisually on NCBI it gives me the desired results but nothing shows up in batch entrez, it says wrong UID. The ids look like this

GRMZM2G365374_T02
GRMZM2G153815_T01
LOC_Os12g14070.1
GRMZM5G802801_T01
AC209784.3_FGT007
Sobic.009G163900.1
GRMZM2G366532_T01
LOC_Os03g16920.1
GRMZM2G366532_T02
Sobic.001G418600.1
GRMZM2G366532_T01
Sobic.006G055600.2
LOC_Os01g62290.2
Sobic.006G055600.1
LOC_Os05g38530.1
LOC_Os01g62290.1
Sobic.003G350700.1
GRMZM2G310431_T01
AC209784.3_FGT007

i also tried converting these ids using biodbnet but how do i know what kind of identifiers are these. i got them from phytozome. somebody please help. thank you

blast sequence phytozome batch entrez ncbi • 3.0k views
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7.4 years ago
GenoMax 142k

Have you tried to use BioMart on the Phytozome site under "tools" menu?

I was able to get sequence using "Current phytozome" --> "Phytozome 11 genomes" --> "Filters" --> "Gene" --> "ID List filter" --> "Transcript name" for the ID's you posted.

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7.4 years ago
ashish ▴ 680

genomax2 thank you very much. i got the sequences using biomart on phytozome. i tried this earlier but was using gene name instead of transcript name.

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Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

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alright i will take care of it from now onwards. i am very new to biostars.

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No problem and welcome to biostars. In addition, if the answer from genomax2 solved your question, please mark the answer as "accepted" to flag this thread as resolved.

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