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This server takes FASTA formatted sequences as input and returns similar sequences from the selected database. All results are returned immediately.
SANSparallel [1] is an MPI implementation of a suffix array neighborhood search client-server. The original SANS method [2] was improved, re-implemented as a client-server, and parallelized. The server can be accessed in a web browser or programmatically.
Web outputs are presented as tables, BLAST-like pairwise alignments, or stacked alignments which can be viewed in Jalview or as sequence logos. Programmatic access enables the building of bioinformatic pipelines, for example, for protein function prediction.
The method is extremely fast and as sensitive as BLAST above 50 % sequence identity (cf. [3]). The performance of SANSparallel was comparable to DIAMOND, LAMBDA and LAST in our benchmarks [1].
Clients
The following applications are powered by the SANSparallel server:- Lazypipe virus discovery and annotation pipeline for NGS data from a variety of samples - free access, installed at CSC. Already picked up, e.g., a new ebolavirus and tick-borne flavivirus + double infections from COVID-19 patients.
- Pannzer2, a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes. Processes bacterial proteomes in minutes and eukaryotic proteomes in an hour.
- AAI-profiler, a fast homology search tool that takes a query proteome (protein sequences in FASTA format) as input and plots the AAI (Average Amino-acid Identity) values of all species in the Uniprot database.
References
- Somervuo P, Holm L (2015) SANSparallel: Interactive homology search against Uniprot. Nucl. Acids Res. 43:W24-W29. PDF
- Koskinen P, Holm L (2012) SANS: High-throughput retrieval of protein sequences allowing 50 % mismatches. Bioinformatics 28, i438-i443
- Benchmarking report from SIB
