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
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
22 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment