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Structural homology guided alignment of cysteine rich proteins

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journal contribution
posted on 11.02.2021, 23:49 by Thomas Shafee, Andrew Robinson, Nicole Van Der Weerden, Marilyn Anderson
© 2016 Shafee et al. Background: Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions. Results: 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. Conclusions: 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).

History

Publication Date

12/01/2016

Journal

SpringerPlus

Volume

5

Issue

1

Article Number

27

Pagination

7p. (p. 1-7)

Publisher

SpringerOpen

ISSN

2193-1801

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The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.

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