Annotation for contigs from de novo assembly

witty · 02-06-2014, 11:16 AM

Hi,

I want to annotate my assembled contigs (from de novo assembly). I used BLASTX and only got 10~20% percentage of hits(evalue=1e-5). Now all my differentially expressed contigs (genes) have no annotation. At least I want to know what these genes are, e.g, signaling, transmembrane etc.

Thanks a lot!
Victoria

themerlin · 02-06-2014, 11:33 AM

I'd give Prokka a try:

http://www.vicbioinformatics.com/software.prokka.shtml

GenoMax · 02-06-2014, 12:00 PM

Provided Victoria is working with a prokaryotic genome

NCBI has a eukaryotic annotation pipeline: http://www.ncbi.nlm.nih.gov/genome/a...n_euk/process/ and a prokaryotic one: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ If I recall right, you will have to make the sequence public though at some point in time if you use these.

Other eukaryotic options (have not used myself):

Pasa: http://pasa.sourceforge.net/
Maker: http://www.gmod.org/wiki/MAKER

dnusol · 02-06-2014, 11:45 PM

I think Blast2GO would also be useful

ChrisAU · 02-07-2014, 02:16 AM

I've also had good experience with Blast2GO, it doesn't require installation and is quite easy to handle. Also, they updated the quite ugly colours of their pie charts

witty · 02-07-2014, 12:30 PM

Hi,

Thank you for your reply. I understand that blast2go (see the below link) just used blast result so basically it won't provide more annotated contigs than BLASTX that I did, is it correct?

https://sites.google.com/a/brown.edu...d/b2g4pipe-2-5

The organism I want to annotate is the protist, Oxyrrhis Marina.

Thank you!
Victoria

Krish_143 · 02-11-2014, 03:10 AM

RAST annotation.
http://rast.nmpdr.org/

dnusol · 02-25-2014, 01:26 AM

Hi Victoria, I guess you could use several databases to increase your chances of annotation. What databases have you used? I don't have experience with protists but in general a good start could be to compare against GenBank and Uniprot's Swiss-Prot and TrEMBL protein databases. Have you tried a less conservative e-value? Also try to download similar species that are annotated to compare directly. This reference may help you

http://www.plosone.org/article/info%...l.pone.0014202

Dave

Birdman · 02-25-2014, 06:44 AM

You can try the Trinotate pipeline. It involves several tools (TransDecoder to get plausible ORFs, PFAM, HMMER, signalIP, tmHMM, RNAmmer) to obtain a quite complete annotation report. They give a lot of details on the website on how to use it.

bastianwur · 03-02-2014, 10:43 AM

Run a gene prediction tool (e.g. prodigal) over it, throw the proteins in InterproScan, and check if you get anything interesting for your analysis.

Might as well be good to know how long the contigs are.
Will not be of much use to annotate stuff, which is considerable less long than 900 bp.

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02-06-2014, 11:16 AM	#1
witty Junior Member Location: RI Join Date: Nov 2013 Posts: 5	Annotation for contigs from de novo assembly Hi, I want to annotate my assembled contigs (from de novo assembly). I used BLASTX and only got 10~20% percentage of hits(evalue=1e-5). Now all my differentially expressed contigs (genes) have no annotation. At least I want to know what these genes are, e.g, signaling, transmembrane etc. Thanks a lot! Victoria

02-11-2014, 03:10 AM	#7
Krish_143 Member Location: Sweden Join Date: Jan 2012 Posts: 45	RAST annotation. http://rast.nmpdr.org/ __________________ Krishna

02-06-2014, 11:33 AM	#2
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	I'd give Prokka a try: http://www.vicbioinformatics.com/software.prokka.shtml

02-06-2014, 12:00 PM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Provided Victoria is working with a prokaryotic genome NCBI has a eukaryotic annotation pipeline: http://www.ncbi.nlm.nih.gov/genome/a...n_euk/process/ and a prokaryotic one: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ If I recall right, you will have to make the sequence public though at some point in time if you use these. Other eukaryotic options (have not used myself): Pasa: http://pasa.sourceforge.net/ Maker: http://www.gmod.org/wiki/MAKER

02-06-2014, 11:45 PM	#4
dnusol Senior Member Location: Spain Join Date: Jul 2009 Posts: 133	I think Blast2GO would also be useful

02-07-2014, 02:16 AM	#5
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	I've also had good experience with Blast2GO, it doesn't require installation and is quite easy to handle. Also, they updated the quite ugly colours of their pie charts

02-07-2014, 12:30 PM	#6
witty Junior Member Location: RI Join Date: Nov 2013 Posts: 5	Hi, Thank you for your reply. I understand that blast2go (see the below link) just used blast result so basically it won't provide more annotated contigs than BLASTX that I did, is it correct? https://sites.google.com/a/brown.edu...d/b2g4pipe-2-5 The organism I want to annotate is the protist, Oxyrrhis Marina. Thank you! Victoria

02-25-2014, 01:26 AM	#8
dnusol Senior Member Location: Spain Join Date: Jul 2009 Posts: 133	Hi Victoria, I guess you could use several databases to increase your chances of annotation. What databases have you used? I don't have experience with protists but in general a good start could be to compare against GenBank and Uniprot's Swiss-Prot and TrEMBL protein databases. Have you tried a less conservative e-value? Also try to download similar species that are annotated to compare directly. This reference may help you http://www.plosone.org/article/info%...l.pone.0014202 Dave

02-25-2014, 06:44 AM	#9
Birdman Member Location: Montreal Join Date: Jan 2014 Posts: 21	You can try the Trinotate pipeline. It involves several tools (TransDecoder to get plausible ORFs, PFAM, HMMER, signalIP, tmHMM, RNAmmer) to obtain a quite complete annotation report. They give a lot of details on the website on how to use it.

03-02-2014, 10:43 AM	#10
bastianwur Member Location: Germany/Netherlands Join Date: Feb 2014 Posts: 98	Run a gene prediction tool (e.g. prodigal) over it, throw the proteins in InterproScan, and check if you get anything interesting for your analysis. Might as well be good to know how long the contigs are. Will not be of much use to annotate stuff, which is considerable less long than 900 bp.