This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Homology and Alignments
Homologues
Using Homologene, I identified several homologues of human HBA1, all of which were in higher vertebrates.
Bos taurus
Gene Name: HBA1
Accession: NC_007326.4
Mus musculus
Gene Name: Hba-a1
Accession: NC_000077.5
Rattus norvegicus
Gene Name: Hba-a2
Accession: NC_005109.2
Gallus gallus
Gene Name: HBAA
Accession: NC_006101.2
Sequence Alignment
This alignment was generated using T-COFFEE [1,2,3].
Another Alignment
This alignment was generated using ClustalW [1,2,4]. There is low homology seen in both of these alignments, which is likely due to the different sources used for the FASTA sequences (i.e. whole genome shotgun sequence vs. mRNA sequence).
Using Homologene, I identified several homologues of human HBA1, all of which were in higher vertebrates.
Bos taurus
Gene Name: HBA1
Accession: NC_007326.4
Mus musculus
Gene Name: Hba-a1
Accession: NC_000077.5
Rattus norvegicus
Gene Name: Hba-a2
Accession: NC_005109.2
Gallus gallus
Gene Name: HBAA
Accession: NC_006101.2
Sequence Alignment
This alignment was generated using T-COFFEE [1,2,3].
Another Alignment
This alignment was generated using ClustalW [1,2,4]. There is low homology seen in both of these alignments, which is likely due to the different sources used for the FASTA sequences (i.e. whole genome shotgun sequence vs. mRNA sequence).
References
- BLAST-EXPLORER helps you building datasets for phylogenetic analysis. Dereeper A., Audic S., Claverie J.M., Blanc G. BMC Evol Biol. 2010 Jan 12;10:8. (PubMed)
- O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel . Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
- T-Coffee: A novel method for fast and accurate multiple sequence alignment.Notredame C., Higgins DG., Heringa J. J Mol Biol. 2000, Sep 8;302(1):205-17. (PubMed)
- CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson J.D., Higgins D.G., Gibson T.J. Nucleic Acids Res. 1994, Nov 11;22(22):4673-80. (PubMed)
