RT Journal Article
SR Electronic
T1 ASM-Clust: classifying functionally diverse protein families using alignment score matrices
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 792739
DO 10.1101/792739
A1 Daan R. Speth
A1 Victoria J. Orphan
YR 2019
UL http://biorxiv.org/content/early/2019/10/03/792739.abstract
AB Rapid advances in sequencing technology have resulted in the availability of genomes from organisms across the tree of life. Accurately interpreting the function of proteins in these genomes is a major challenge, as annotation transfer based on homology frequently results in misannotation and error propagation. This challenge is especially pressing for organisms whose genomes are directly obtained from environmental samples, as interpretation of their physiology and ecology is often based solely on the genome sequence. For complex protein (super)families containing a large number of sequences, classification can be used to determine whether annotation transfer is appropriate, or whether experimental evidence for function is lacking. Here we present a novel computational approach for de novo classification of large protein (super)families, based on clustering an alignment score matrix obtained by aligning all sequences in the family to a small subset of the data. We evaluate our approach on the enolase family in the Structure Function Linkage Database.Availability and implementation ASM-Clust is implemented in bash with helper scripts in perl. Scripts comprising ASM-Clust are available for download from https://github.com/dspeth/bioinfo_scripts/tree/master/ASM_clust/