Top Features
SeqQuests is a new collection of bioinformatics software.
- Optimised for Apple silicon: A fast Smith-Waterman amino acid sequence comparison.
- Dual architecture: Scriptable command-line utilities (python) with optional web-browser/API-endpoint interfaces
- ~18 twilight zone findings: These suggest database annotation updates.
About SeqQuests
Building open bioinformatics software - using composable pieces.
Code is on GitHub.
SeqQuests
Smith Waterman
Running for 36 hours the flagship module of SeqQuests performed an all-on-all Smith-Waterman comparison of UniProt Swiss-Prot (~570,000 sequences) finding many relationships between proteins in the process
Example Finding: Honeybee Prohormone-3 is annotated as membrane-bound. SeqQuests found it aligns with a secreted ant ortholog - suggesting the protein is secreted, not membrane-anchored. Proposed update:
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000250|UniProtKB:E2ADG2}.
CC -!- SEQUENCE CAUTION: The sequence 1-88 may be artifactual. An
CC alternative translation initiation at Met-84 is supported by
CC RefSeq XP_001122204 and at Met-89 by sequence similarity to E2ADG2.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ITG-like peptide family.
CC {ECO:0000305}.
Additional Tools
The software library additionally includes work on:
- Displaying sequence composition bias
- Browsing Swiss-Prot feature tables with a domain viewer
- Navigating a tree of protein similarities
- Kabsch 3D alignment