Transcript annotation software

Kennels · 01-05-2012, 08:47 PM

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,

arshah18 · 01-05-2012, 10:01 PM

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

huangjun · 01-05-2012, 11:17 PM

Maybe iprscan can help you, iprscan can make the GO annotation! Or you can try the blast2go!

westerman · 01-06-2012, 06:45 AM

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.

colindaven · 01-09-2012, 07:57 AM

BlastP vs Uniprot has worked quite nicely for us (bacterial genomes and transcriptome)

tboothby · 01-09-2012, 08:56 AM

Quote:

Originally Posted by westerman

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.

Kennels · 01-09-2012, 03:44 PM

thanks everyone.

westerman · 01-10-2012, 11:03 AM

Quote:

Originally Posted by tboothby

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.

marnilush · 01-11-2012, 08:07 AM

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

angeloulivieri · 09-06-2014, 02:30 AM

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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01-05-2012, 08:47 PM	#1
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	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 08:48 PM. Reason: typos

01-09-2012, 03:44 PM	#7
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	thanks everyone. Last edited by Kennels; 01-09-2012 at 03:53 PM.

01-05-2012, 10:01 PM	#2
arshah18 Junior Member Location: Delhi Join Date: Jan 2012 Posts: 1	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

01-05-2012, 11:17 PM	#3
huangjun Member Location: Wuhan China Join Date: Dec 2011 Posts: 13	Maybe iprscan can help you, iprscan can make the GO annotation! Or you can try the blast2go!

01-06-2012, 06:45 AM	#4
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	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.

01-09-2012, 07:57 AM	#5
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	BlastP vs Uniprot has worked quite nicely for us (bacterial genomes and transcriptome)

01-11-2012, 08:07 AM	#9
marnilush Member Location: Berlin Join Date: Nov 2009 Posts: 12	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

09-06-2014, 02:30 AM	#10
angeloulivieri Member Location: Italy Join Date: Jul 2012 Posts: 30	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)...