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Old 03-22-2010, 11:55 PM   #1
jjk
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Default Looking for Annotation software

At the moment i have more or less a chloroplast genome assembled. What i could do now is get al the ORF's and blast it and obtain the names by using for example BLAST2GO. The problems i am facing with that is when i take a ORF it might also be present somewhere else. And when i realign the results back it does not match the region i had before. ( Can do it all 1 by one but that will take ages!)

My question is now is the following possible:

Give a program the chloroplast sequence in fasta.

Let the program look for ORF's

Blast the ORF's and annotate the location

Send me the file.

Thanks for the help
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Old 03-23-2010, 03:27 AM   #2
tcezard
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Have you tried Artemis.
It can detect ORF and annotate them and can read .bam file
http://www.sanger.ac.uk/resources/software/artemis/

Tim
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Old 03-23-2010, 03:58 AM   #3
jjk
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Thanks im looking into it at the moment. But does this program need a database located at our place or is NCBI also possible for mass blasting of all the ORF's and annotation. Still reading the manual though
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Old 03-23-2010, 04:08 AM   #4
maubp
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I've done this kind of workflow with Python scripts: take FASTA genome, find ORFs, BLAST them, produce a crudely annotated GenBank or EMBL file, give this to our Biologists to look at in Artemis or their tool of choice. This gives me the freedom to tweak everything (for example how to handle alternative start codons, which BLAST database to use, etc).
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Old 03-23-2010, 04:23 AM   #5
steven
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Quote:
Originally Posted by jjk View Post
At the moment i have more or less a chloroplast genome assembled. What i could do now is get al the ORF's and blast it and obtain the names by using for example BLAST2GO. The problems i am facing with that is when i take a ORF it might also be present somewhere else. And when i realign the results back it does not match the region i had before. ( Can do it all 1 by one but that will take ages!)

My question is now is the following possible:

Give a program the chloroplast sequence in fasta.

Let the program look for ORF's

Blast the ORF's and annotate the location

Send me the file.

Thanks for the help
Maybe this previous thread could help
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Old 03-23-2010, 05:28 AM   #6
jjk
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Through artemis i got the ORF's and through Run > Pfam Search i get the correct name for the ORF. But how to do this for all my ORF's and automatically?

Found the readme.. (my bad)

Searching and Using Local Sequence Databases (Optional)

Will look into that

###
Downloaded all the blast software and placed it in the package dir from Artemis.

But when i use the GUI in the mac environment, select the ORF's, Run fasta on selected future against %uniprot it gives me the login screen... I hoped i could make a link against the NCBI database but is this even possible cause i dont have any data myself because this is a "new" species we are working on

Last edited by jjk; 03-23-2010 at 09:17 PM. Reason: ###
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