Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST

2010 ◽  
Vol 17 (6) ◽  
pp. 819-823 ◽  
Author(s):  
Mats Aspnäs ◽  
Kimmo Mattila ◽  
Kristoffer Osowski ◽  
Jan Westerholm
Keyword(s):  
Homology Search ◽  
Code Optimization ◽  
Sequence Database ◽  
Search Tool

scholarly journals NeuroBlast: a 3D spatial homology search tool for gene expression

2007 ◽  
Vol 8 (S2) ◽  
Author(s):  
Lydia Ng ◽  
Chris Lau ◽  
Rob Young ◽  
Sayan Pathak ◽  
Leonard Kuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Homology Search ◽  
Search Tool

scholarly journals COSS: A fast and user-friendly tool for spectral library searching

2019 ◽  
Author(s):  
Genet Abay Shiferaw ◽  
Elien Vandermarliere ◽  
Niels Hulstaert ◽  
Ralf Gabriels ◽  
Lennart Martens ◽  
...  
Keyword(s):  
Scoring Functions ◽  
Sequence Database ◽  
Spectral Library ◽  
Data Formats ◽  
Large Databases ◽  
Search Tool ◽  
Spectral Searching ◽  
Spectral Libraries ◽  
User Friendly ◽  
Sequence Database Search

ABSTRACTSpectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tool. Our comparison showed that COSS more reliably identifies spectra and is faster than other spectral library searching tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.

scholarly journals Best BLAST hit alone cannot be used as evidence of fraud

2021 ◽  
Author(s):  
Naiara Rodriguez-Ezpeleta ◽  
Natalia Diaz-Arce
Keyword(s):  
Species Identification ◽  
Dna Markers ◽  
Sequence Database ◽  
Molecular Tools ◽  
Basic Tool ◽  
Fish Products ◽  
Search Tool ◽  
Fish Product

In a recent study, Blanco-Fernandez et al. applied molecular tools to authenticate fish products and conclude evidence of 'worrying international fraud'. They revealed mislabeling in recognizable and unrecognizable fish products labeled as anchovy, hake and tuna commercialized by European companies. Their analyses consisted on extracting DNA from the fish product to be authenticated followed by amplification and sequencing of a suite of DNA markers and on comparing the resulting sequences to the GenBank sequence database using BLAST (Basic Tool Alignment Search Tool) (https://blast.ncbi.nlm.nih.gov/Blast.cgi). By carefully reanalyzing their data, we identify errors in their species identification and conclude that best BLAST hit alone cannot be used as evidence of fraud.

scholarly journals GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e36060 ◽  
Author(s):  
Shuji Suzuki ◽  
Takashi Ishida ◽  
Ken Kurokawa ◽  
Yutaka Akiyama
Keyword(s):  
Homology Search ◽  
Search Tool

scholarly journals A sensitive short read homology search tool for paired-end read sequencing data

2017 ◽  
Vol 18 (S12) ◽  
Author(s):  
Prapaporn Techa-Angkoon ◽  
Yanni Sun ◽  
Jikai Lei
Keyword(s):  
Homology Search ◽  
Sequencing Data ◽  
Short Read ◽  
Search Tool

Comet: An open-source MS/MS sequence database search tool

PROTEOMICS ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 22-24 ◽  
Author(s):  
Jimmy K. Eng ◽  
Tahmina A. Jahan ◽  
Michael R. Hoopmann
Keyword(s):  
Open Source ◽  
Database Search ◽  
Sequence Database ◽  
Search Tool ◽  
Sequence Database Search

scholarly journals Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W143-W146 ◽  
Author(s):  
R. Bhadra ◽  
S. Sandhya ◽  
K. R. Abhinandan ◽  
S. Chakrabarti ◽  
R. Sowdhamini ◽  
...  
Keyword(s):  
Web Server ◽  
Protein Domains ◽  
Homology Search ◽  
Remote Homology ◽  
Search Tool
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