SANS: high-throughput retrieval of protein sequences allowing 50% mismatches

Abstract

Motivation: The genomic era in molecular biology has brought on a rapidly widening gap between the amount of sequence data and first-hand experimental characterization of proteins. Fortunately, the theory of evolution provides a simple solution: functional and structural information can be transferred between homologous proteins. Sequence similarity searching followed by k-nearest neighbor classification is the most widely used tool to predict the function or structure of anonymous gene products that come out of genome sequencing projects.Results: We present a novel word filter, suffix array neighborhood search (SANS), to identify protein sequence similarities in the range of 50–100% identity with sensitivity comparable to BLAST and 10 times the speed of USEARCH. In contrast to these previous approaches, the complexity of the search is proportional only to the length of the query sequence and independent of database size, enabling fast searching and functional annotation into the future despite rapidly expanding databases.Availability and implementation: The software is freely available to non-commercial users from our website http://ekhidna.biocenter.helsinki.fi/downloads/sans.Contact: liisa.holm@helsinki.fi.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

“…First, MP reads and PacBio reads were aligned against existing scaffolds using BWA51 and an in-house SANS aligner52, respectively. After subsequent filtering, the linkage map was used as a guide to determine the most reliable path between the scaffolds to yield individual superscaffolds.…”

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“…Although the group members had experience in sequencing and assembling microbial and fungal genomes, performing automatic and manual annotation as well as developing assembly and annotation methods, the M. cinxia genome was the first large genome project for all of us. In addition to the genome and the genome paper, it also yielded new scaffolding , read error correction (Salmela 2010, Salmela & Schröder 2011, functional annotation (Koskinen et al 2015), orthology prediction (Ta et al 2011, Koskinen & Holm 2012, linkage mapping (Rastas et al 2013), and RNA-seq (Kvist et al 2015) and RAD-seq (Rastas et al 2013) library preparation methods. The M. cinxia genome project was also a pioneering project in the sense that it gave many groups in Finland the confidence to initiate a similar investigation as exemplified by the ongoing silver birch (J. Salojärvi unpubl.…”

Scaling VM Deployment in an Open Source Cloud Stack

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