I want to compare the scaffolds with the reference sequence and analyze the order and orientation. Can any body help me in this? also can we close gaps in the scaffolds using bioinformatics approach
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Hi,
This maybe a bit late, I was just browsing the 454 forum for something else...anyways, if its still of use:
For comparing scaffolds with a reference genome you can:
Use roche reference mapper (part of newbler), MAUVE, Artemis comparison tool and contig aligner an online program http://nbc11.biologie.uni-kl.de/fram...ontig_aligner/.
They involve you uploading/submitting your reference genome as fasta file and your concatentated scaffolds (merge all your scaffolds into a single fasta file) or individually uploading/submitting them as a seperate 'genome/s'. Note the positions so you can work out the order.
For gap closing informatically i don't know of any sure way of doing it, i've tried by blast searching and using contig aligner to compare the unmapped contigs to the reference genome to see where they match, for us the ones that were confidently mapped were experimentally confirmed. This in some instances closed gaps but in the majority reduced the gap size for experimental closure, primer walking etc... But again i'm not sure of a fool-proof method to do it bioinformatically...
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, Today, 08:06 AM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Today, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
||
Started by seqadmin, 04-29-2024, 10:49 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
04-29-2024, 10:49 AM
|
||
Started by seqadmin, 04-25-2024, 11:49 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
04-25-2024, 11:49 AM
|
Comment