Looking for Annotation software

jjk · 03-22-2010, 11:55 PM

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

tcezard · 03-23-2010, 03:27 AM

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

jjk · 03-23-2010, 03:58 AM

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

maubp · 03-23-2010, 04:08 AM

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).

steven · 03-23-2010, 04:23 AM

Quote:

Originally Posted by jjk

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

jjk · 03-23-2010, 05:28 AM

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

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03-22-2010, 11:55 PM	#1
jjk Member Location: Brisbane Join Date: Nov 2009 Posts: 21	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

03-23-2010, 05:28 AM	#6
jjk Member Location: Brisbane Join Date: Nov 2009 Posts: 21	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: ###

03-23-2010, 03:27 AM	#2
tcezard Member Location: Edinburgh Join Date: Dec 2008 Posts: 13	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

03-23-2010, 03:58 AM	#3
jjk Member Location: Brisbane Join Date: Nov 2009 Posts: 21	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

03-23-2010, 04:08 AM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	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).