Question: Looking for an annotation tool
2
gravatar for nkuo
4.3 years ago by
nkuo20
nkuo20 wrote:

So I am looking for genome annotation tools that fits one or more of following requirement

  1. start with current state of annotation (as in the tools can give different analysis in comparison to the old one if we update the database)

  2. Manual annotation comes with text-mining tool that grabs information from literature and papers

  3. Does computational annotation

UniProt seems fits the all three requirement but it seems only annotate proteins. We are also looking for tools that annotate RNA. Also, I am looking for multiple tools and they don't have to fit all the requirement list above. I am trying to see I can compare each tool's method on how their step of annotation so I can get more understanding in this field.

Thank You

Please disregard this as it was on my old edit just (after did some research I find some tools such as BLAST2GO, or Prokka that may fits some of the requirement here However, based on my limited knowledge on this field I really don't know if I am on the right track. I wonder if anyone here can provide name of some tools that fits the requirement, or a site that can look for different kind of genomic annotation software.)

ADD COMMENTlink modified 4.3 years ago by YaGalbi1.5k • written 4.3 years ago by nkuo20
1

Annotation: look at these tools;

http://geneontology.org/page/annotation-tools-downloads-and-beyond

http://go.princeton.edu/ - also gene ontology

You will find many choices below:

https://omictools.com/genome-annotation-category

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by natasha.sernova3.7k
1

Also this,

https://omictools.com/gene-set-analysis-category

ADD REPLYlink written 4.3 years ago by EagleEye6.7k

I already looked up on GO, but that link of omictools are very helpful. I will get my hand on that now

ADD REPLYlink written 4.3 years ago by nkuo20
3
gravatar for YaGalbi
4.3 years ago by
YaGalbi1.5k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.5k wrote:

Have you considered Artemis? http://www.sanger.ac.uk/science/tools/artemis

ADD COMMENTlink written 4.3 years ago by YaGalbi1.5k

I actually did. It is on my list of annotation tool but for this one it is really hard for me to understand. I am assuming this is manual annotation tool but not completely sure about it

ADD REPLYlink written 4.3 years ago by nkuo20
2

I created the following protocol for using Artemis - feel free to edit and use as you wish: https://www.dropbox.com/s/u0kmzfq5hpt7ygv/Using%20artemis.docx?dl=0

The user manual is here: ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf

ADD REPLYlink written 4.3 years ago by YaGalbi1.5k

that's really awesome. Thanks for the help

ADD REPLYlink written 4.3 years ago by nkuo20
2
gravatar for EagleEye
4.3 years ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:

GeneSCF is based on real-time retrieval of information (uses current available functional database from Gene Ontology, KEGG or Reactome) to perform enrichment analysis.

Gene Set Clustering based on Functional annotation (GeneSCF)

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by EagleEye6.7k

Again thanks for the answer, after asking my supervisor today he told me this looks more like network annotation tool but he could be wrong but if not that is not what we are looking for. Do you have some other suggestion?

ADD REPLYlink written 4.3 years ago by nkuo20
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