In Jalview, how can I colour just the nucleotides that are different between sequences

I have 3 sequences in Jalview, they are around 90% identity when doing a single alignment against each other, how can I show with colour which bases differ? The nucleotide options colours all bases...

alignment jalview

• 1,502 views • link

written 8.2 years ago by SaltedPork

0 answers

No answers yet.

More posts like this

Tool for aligning short protein sequences
written 3.5 years ago by SaltedPork

Hi, I have a file that looks like: >ref_frame=1 XFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >ref_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >ref_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR >read1_frame=1 FFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >read1_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >read1_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR I want to do a …
Using different tools for different database sequences to identify antibiotic resistance genes.
written 5.5 years ago by dymphan.17phd •

I have obtained nucleotide and protein genes using PRODIGAL tool from assembled contigs in a illumina sequenced metagenomic sample. I need to search against three …
One gene shows alignment with core sequences as well as with accessory gene sequences at 50% identi…
written 6.3 years ago by sharmatina189059 •

Hi I have done pan-genome analysis with 0.5% identity cutoff using BPGA tool. and it has given me core reference sequence, accessory reference file and …
Interpret genome alignment results
written 6.8 years ago by el97004 •

Hi all! I assembled two different genomes and wanted to see how similar they are on both nucleotide and protein levels so I aligned their …
global alignment using needleall
written 11.0 years ago by Quak

I am using EMBOSS implementation of needleman to build a similarity matrix of 50k nucleotide reads against each other; 1. I don't know how to …
which factors help to select positive blastx result?
written 11.6 years ago by Kurban

Hello guys! I have BLASTXed a query file (which contain more than 140000 nucleotide sequences) with a db file (which contain more than 1400 polypeptide …
create a legend in ggplot2 plot
written 11.9 years ago by Assa Yeroslaviz

Hi, I have a data.frame which I would like to plot using the ggplot2 package. This is what i am doing: ``` myBreaks <- c(seq(0,0.001, …
very poor alignment on total RNA data from exosome
written 12.0 years ago by nextgenseq.bioinfo •

Hello Gentle People, I have human RNA-seq data obtained from sequencing a total RNA library prepared using Nugen ovation kit 2 from exosome sample. I …
Multiple Alignment: Protein Or Nucleotide Sequence?
written 12.9 years ago by tomas.iesmantas •

I'm quite new in bioinformatics area, but will try to describe my problem accurately. I have protein and corresponding nucleotide sequences. I use multiple alignment …
Analysis Data And Msa
written 14.5 years ago by Hanan •

Hi : I have a file of Data includes 20 proteins, each 10 proteins belongs to different class. My goal is to extract the similarities …