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Old 01-05-2012, 07:47 PM   #1
Kennels
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Default Transcript annotation software

Hello,

I have a transcriptome assembly, and would like to just very quickly annotate the transcripts - it doesn't have to be that good as this is just a first pass.
Can someone point me to a software where I can just simply specify my assembly (which is just a fasta file) and it will try and annotate each transcript based on some databases.

I have done a search (e.g Ensembl's genebuild) but I can't seem to find a simple 'plug and play, one-stop' program - or am I simplifying the process too much?

Thanks,

Last edited by Kennels; 01-05-2012 at 07:48 PM. Reason: typos
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Old 01-05-2012, 09:01 PM   #2
arshah18
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hi,
you can use Cufflinks.
http://cufflinks.cbcb.umd.edu/
It is a bit laborious work. you can take some help from this paper as well.
http://www.nature.com/nbt/journal/v2.../nbt.1621.html

Thanks
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Old 01-05-2012, 10:17 PM   #3
huangjun
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Maybe iprscan can help you, iprscan can make the GO annotation! Or you can try the blast2go!
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Old 01-06-2012, 05:45 AM   #4
westerman
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blast2go is what we use for de-novo transcriptomes. Unfortunately it can take some time to run because it does blast searches and then GO lookup. Depends on how many transcripts you have but expect a day or two of processing time.
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Old 01-09-2012, 06:57 AM   #5
colindaven
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BlastP vs Uniprot has worked quite nicely for us (bacterial genomes and transcriptome)
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Old 01-09-2012, 07:56 AM   #6
tboothby
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Quote:
Originally Posted by westerman View Post
blast2go is what we use for de-novo transcriptomes. Unfortunately it can take some time to run because it does blast searches and then GO lookup. Depends on how many transcripts you have but expect a day or two of processing time.
Do you know if B2G output files can be used (or converted and then used) with mapping programs like tophat/bowtie?

I ask because I have a de novo transcriptome that I want to annotate and then use as a reference to map of sequencing reads to.

I have figured out how to do all the above, except generate an annotation file to feed tophat/bowtie. Any ideas anyone?

For the original poster, blast2go is pretty easy to use. To increase speed you can do the BLAST searcher ahead of time using a local machine (just be sure to save output in xml format) and then load the blast results into blast2go.
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Old 01-09-2012, 02:44 PM   #7
Kennels
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thanks everyone.

Last edited by Kennels; 01-09-2012 at 02:53 PM.
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Old 01-10-2012, 10:03 AM   #8
westerman
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Quote:
Originally Posted by tboothby View Post
Do you know if B2G output files can be used (or converted and then used) with mapping programs like tophat/bowtie?

I ask because I have a de novo transcriptome that I want to annotate and then use as a reference to map of sequencing reads to.

I have figured out how to do all the above, except generate an annotation file to feed tophat/bowtie. Any ideas anyone?
I had a person ask me this question today. I told him that I have never done such a conversion but I suspect that it could be done with a custom program. Certainly the data is there albeit in different files.
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Old 01-11-2012, 07:07 AM   #9
marnilush
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If you are working on a plant transcriptome, you could also use the
mercator tool which assigns MapMan Bins to each of your sequences.
The web interface accepts only relatively small datasets, but there is no
problem in annotating larger (i.e. whole transcriptome) datasets. Just contact
me directly and we can arrange this (of course we will treat your data
confidentially). The advantage is, that the tool is quite fast (usually around 2-3
days for a full transcriptome of 30000 transcripts) and the output is directly
usable as mapping files in MapMan and PageMan for further visualization
and exploration of e.g. RNA-Seq data.

If you are interested visit: http://mapman.gabipd.org/
and or contact me directly: lohse_at_mpimp-golm.mpg.de

cheers
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Old 09-06-2014, 01:30 AM   #10
angeloulivieri
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You may want to try Annocript. You can google it. It executes blast software and can predict putative coding and long non-coding RNA. The output is a tabular one and you can use it with other script you can do. Plot are also shown.

If you install, it will download uniprot databases and build a mysql database which you can use also. Later it will execute everything on you machine. It is not dependent from the connection.

The only problem is that it can run only on unix based systems (mac, linux)...
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