clustering sequences in two different assemblies to find similarities based on sequence
Dear all,
I have two assembly, and I want to cluster of each sequence in two assemblies to find how similar the two assembly in terms of sequence. I used cd-hit-est-2d. I also want to use another tool for this. Any recommendation?
Thank you
• 2,013 views
•
link
updated
by
renjukrishna13 •
•
written
by
Mehmet
•
written
by
Mehmet
1 answer
The other strategy I would recommed is to translate and get the peptides in all frames and do a protein level clustering. You could use latest tools like MMseq, https://github.com/soedinglab/MMseqs2 to do the clustering .
• 0 views
•
link
written
by
renjukrishna13 •
Log in to answer this question.
More posts like this
-
Efficiently Converting CD-HIT-EST Clusters into .fasta Files
written by mtsrn •
-
Can I use CD-HIT package for shotgun sequencing data (metagenomic) comparsion?
written by arshad1292 •
-
CD-HIT: representative sequence vs consensus sequence
written by rDNA •
-
Can BBTools Dedupe be used in transcriptome assembly clustering ?
written by VineethVenumadhavan •
-
CD-HIT-EST-2D how to get more of miRNAs
written by silvernonferous •
-
About clustering genes isoforms in RNA-Seq
written by Lucas Peres
-
Low sequence similarity between two samples of the same species
written by Mehmet
-
parsing cd-hit result
written by ####
-
overlap sequences in two assemblies
written by Mehmet
-
Cd-Hit-Est-2D Segmentation Fault
written by Mariam Rizkallah •
Nucmer or mummer is just what you are lookingfor (I think)