Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
MEGAN view alignment problems OllyBolly Bioinformatics 2 07-08-2013 12:29 AM
sequence alignment tool selection question slny Bioinformatics 2 06-02-2011 02:36 PM
view alignment and assembling results with UCSC genome browser? dicty Bioinformatics 1 03-04-2011 08:38 AM
samtools view error: CIGAR and sequence length are inconsistent (tophat/bowtie) glacierbird Bioinformatics 2 06-29-2010 02:58 AM

Thread Tools
Old 07-31-2015, 01:08 PM   #1
Location: Massachusetts

Join Date: Jan 2014
Posts: 12
Default Best tool to view sequence alignment?

I blasted my de novo assembled RNA-Seq transcriptome for a particular protein using tblastn, and found three transcripts similar to this protein. The best hit matches with a 50% percent identity (e value 1E-11).

I would like to create a figure displaying the sequence alignment with the greatest match to this protein, or all three transcripts that matched. I used ClustalW and Clustal Omega to align the sequences of my transcripts to the mRNA transcripts of the known protein I pulled off of NCBI but I don't like the aesthetics of the output and I'm not sure if this is the best way to do it.

Any suggestions on a nice way to succinctly display sequence homology between my transcripts and this protein?
cacti is offline   Reply With Quote
Old 07-31-2015, 04:01 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080

Have you looked at tools here:

You can also try MEGA (

The 50% identity over how many AA? You may only be looking at a similar/identical domain.
GenoMax is offline   Reply With Quote

rna-seq, sequence alignment, sequence homology, tblastn, visualization tools

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:40 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO