Sentence examples for used for sequence searching from inspiring English sources

A local implementation of NCBI BLASTX was used for sequence searching.

Each member and pattern pair was used for sequence searches using PHI-BLAST.

Online tools supported by NCBI were used for sequence search and alignment.

Two popular methods, PSI-BLAST and PHI-BLAST, from the BLAST 2.2.23+ package, were used for sequence searches (ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.23/ncbi-blast-2.2.23+-x64-linux.tar.gz) (see Figure 1 for a flow-chart).

The Peptidase Database, MEROPS (http://merops.sanger.ac.uk/) and the clustalw2 application in EBI (http://www.ebi.ac.uk/Tools/msa/clustalw2/) were used for sequence similarity searching and analysis of the SltB protease domain.

The MASCOT search engine (version 2.4) was used for peptide sequence searching against the UniProt database, setting the following restrictions: Homo sapiens taxonomy (Human), parent ion tolerance ±20 ppm, MS/MS error tolerance ±0.1 Da, alkylation of cysteine residues (fixed modifications), oxidation of methionine (variable modifications), and two potentially missed trypsin cleavages.

Here, HMMs are used for sensitive sequence searching across 1483 genomes across the tree of life.

BLAST [62] using a threshold of 1e-10 was used for sequence similarity searches.

In Mode-1, PSI-BLAST [ 19] was used for sequence similarity searches.

The BLAST program (Altschul SF [ 13]) was used for sequence homology searches within the database.

BlastP (Altschul et al. 1990) with a low complexity mask was used for sequence similarity searches.