Structural homology guided alignment of cysteine rich proteins

SpringerPlus
Thomas M A ShafeeMarilyn A Anderson

Abstract

Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions. Here we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequences can then be aligned using any standard algorithm. Finally the barcodes are replaced with the original columns to yield an alignment which requires the minimum of manual refinement. Using structural homology information to constrain sequence alignments allows the alignment of highly divergent, repetitive sequences that are poorly dealt with by existing algorithms. Tools are provided to perform this method online using the CysBar web-tool (http://CysBar.science.latrobe.edu.au) and offline (python script available from http://github.com/ts404/CysBar).

References

Mar 20, 1992·Journal of Molecular Biology·S Pascarella, P Argos
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jul 17, 1998·Current Opinion in Structural Biology·R B Russell, C P Ponting
Aug 11, 2000·Toxicon : Official Journal of the International Society on Toxinology·D J CraikC Waine
Sep 12, 2001·Journal of Structural Biology·N V Grishin
Oct 24, 2001·Bioinformatics·P Fariselli, R Casadio
Jun 13, 2003·Bioinformatics·J D ThompsonO Poch
May 19, 2006·Nucleic Acids Research·Saikat ChakrabartiStephen H Bryant
Jul 18, 2006·Nucleic Acids Research·Alessio CeroniPaolo Frasconi
May 9, 2008·Genome Research·Camilla M WhittingtonKatherine Belov
Jan 31, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kevin LiuTandy Warnow
Jun 2, 2009·Current Opinion in Structural Biology·Hitomi Hasegawa, Liisa Holm
Aug 25, 2009·BMC Evolutionary Biology·Bhakti Dwivedi, Sudhindra R Gadagkar
May 12, 2010·Nucleic Acids Research·Liisa Holm, Päivi Rosenström
Oct 26, 2010·Asian Journal of Andrology·Adam J KoppersMoira K O'Bryan
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Dec 1, 2011·Nucleic Acids Research·Zheng ZhangHui Liu
Dec 30, 2011·Current Pharmaceutical Design·Jérôme Gracy, Laurent Chiche
Jan 10, 2012·Annual Review of Biophysics·Deborah Fass
May 23, 2012·PloS One·Leonid V Bystrykh
Mar 22, 2014·European Journal of Medicinal Chemistry·Susan E NorthfieldDavid J Craik

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Citations

Jun 15, 2016·Molecular Biology and Evolution·Thomas M A ShafeeMarilyn A Anderson
Aug 14, 2018·Bioinformatics·Thomas Shafee, Marilyn A Anderson
Aug 26, 2016·Cellular and Molecular Life Sciences : CMLS·Thomas M A ShafeeMark D Hulett

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Software Mentioned

Clustal Omega
Unix
cysbar
fasta
MacOS
Windows
xlsx
DALI
Excel
BLAST

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