Learn to use the ClustalW2 resource at the EBI Toolbox site for performing multiple sequence alignments, or MSA. MSA allow us to analyze the evolutionary relationship between species on a molecular sequence level. As well, multiple sequence alignments can help us to identify functionally important positions in a sequence family by simply looking at the conservation of positions or motifs within the sequence data.
You will learn:
This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:
BLAST: Basic Local Alignment and Search Tool
FASTA: FASTA sequence algorithm
Entrez Gene: NCBI's Entrez tool for gene-centric information
Primer3: Pick primers from a DNA sequence.
DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools
VISTA: Tools for Comparative Genomics
RefSeq: Provides molecular sequence records to help locate gene and protein data.
EBI : This category includes all resources maintained at the European Bioinformatics Institute (EBI)
Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.
What's the Answer? (publication quality alignment images): This week's highlighted question is from the Bioinformatics subreddit. And I'm using it because it made me laugh. I dare someone to name their alignment tool "Fancy Pants". That said, it did provide li...
Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization: The multiple sequence alignment editing question recently on our What's the Answer? feature was popular. We have covered MSA editors in the past, and we include a bit on Jalview in our Clustal tutorial...
Otto West: Apes don't read [genomics]: Otto West: Apes don't read philosophy. Wanda: Yes they do, Otto. They just don't understand it. --A Fish Called Wanda Some of you remember that last year we were treated to a strange case of DNA denial...
Tip of the Week: Tweaking those alignments: This week's tip introduces a nice feature and tool of the Viral Bioinformatics Resource Center (VBRC). There are a lot of great tools at the VBRC to search and analyze hundreds of viral genomes. Most, ...
Recent BioMed Central research articles citing this resource
Qiao Xin et al., Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear ( Pyrus bretschneideri ) and five other Rosaceae species. BMC Plant Biology (2015) doi:10.1186/s12870-014-0401-5
Filipski Alan et al., Phylogenetic placement of metagenomic reads using the minimum evolution principle Selected articles from the 2nd International Genomic Medicine Conference (IGMC 2013): Genomics 2nd International Genomic Medicine Conference (IGMC 2013). BMC Genomics (2015) doi:10.1186/1471-2164-16-S1-S13
Cordiali-Fei Paola et al., Analysis of the ORFK1 hypervariable regions reveal distinct HHV-8 clustering in Kaposi’s sarcoma and non-Kaposi’s cases. Journal of Experimental Clinical Cancer Research (2015) doi:10.1186/s13046-014-0119-0
Sharma Deepansh et al., Isolation and functional characterization of novel biosurfactant produced by Enterococcus faecium Biomedical and Life Sciences. SpringerPlus (2015) doi:10.1186/2193-1801-4-4
Wang Juanjuan et al., Molecular characterization of a defensin gene from a hard tick, Dermacentor silvarum. Parasites Vectors (2015) doi:10.1186/s13071-014-0625-0