What is the best way to annotate large number of contains from a eukaryote. BlastX is going to take a long time. I was wondering if FgeneSH will be a better first step?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
What is it exactly that you want to do?
It sounds like you want to gene prediction and annotation in one run which doesn't work.
Do gene prediction first (here is a small list of programs http://en.wikipedia.org/wiki/List_of...ction_software). For eukaryotes I prefer augustus or genemark.
For gene annotation you can use something like Blast2GO which is very easy to use. But it takes some time...
-
Fgenesh worked very well for my needs as a first step to identify potential genes. To actually annotate, fgenesh++ would be needed but I have not been able to try that out with my scaffolds (anyone have any experience with this program?) My workflow is to import the fgenesh results into webapollo and then do the rest of the annotation steps manually:
http://www.westga.edu/~lkral/poster/PAG-poster.pdfLast edited by lkral; 10-17-2014, 07:57 AM.
Comment
-
Depends how long the contigs are. It is likely that even long contigs (over 10 Kb) will contain only partial genes. But as long as you are not trying to carry out whole genome comparisons you can assemble whole genes of interest from the partial genes in these contigs (as long as these are single copy genes).
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
Yesterday, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 08:18 AM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 08:18 AM
|
||
Started by seqadmin, Yesterday, 08:04 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 08:04 AM
|
||
Started by seqadmin, 06-03-2024, 06:55 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-03-2024, 06:55 AM
|
||
Started by seqadmin, 05-30-2024, 03:16 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
05-30-2024, 03:16 PM
|
Comment