I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX, ClusTR but could not find the optimal solution. I want to do clustering as like CD-Hit does to reduce dataset but based on sequence similarity rather that sequence identity.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
-
So you want to group by functional similarity?
You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68
I can provide you with file formats/tips if needs beLast edited by JackieBadger; 07-09-2013, 03:55 AM.
Comment
-
Thanks, it seems interesting and I planned to use it later as currently I am not focused on functional similarity!
Originally posted by JackieBadger View PostSo you want to group by functional similarity?
You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68
I can provide you with file formats/tips if needs be
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