Tweet
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
-
-
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...
-
Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
Comment