We have used the SMRT(Pacific Biosciences) sequencing system PacBio RS II to generate cDNA sequences. After isoform-level clustering, polishing and trimming of raw data, non-redundant contigs were obtained. Also with MatchAnno, we have got the isoforms's annotiations? But there still some isoforms located outside of the known genes, so we want to do the new gene prediction analysis. But the tools we found can only be used to analysis the short reads or the short+long reads. So is there any tools do the analysis with only pacbio Iso-seq data?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
To predict new gene functions there are a few ideas besides what BoHan said:
--- plain BLAST to NR to find homologs
--- PFAM or protein domain searches
(you can try using ANGEL [https://github.com/PacificBiosciences/ANGEL] to translate first into ORF)
There's also a tool called BLAST2GO (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375974/) but I haven't used it myself. The author Ana Conesa (U Florida) is actually developing a new pipeline for Iso-Seq for functional annotation, but it's not quite on the market yet...
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment