Sentence examples for cost existence from inspiring English sources

For this paper, the peptides predicted by [ 6] were used to interrogate the 2007 version of the NCBI nonredundant green plant protein and translated nucleotide databases [ 34] using the pBLASTn algorithm with a setting of Expect threshold of 20000, word size 2, Matrix Pam 30, Gap cost Existence: 2, Extension: 1 [ 40].

To analyze the synteny of TOR and flanking regions, we constructed a database of one TOR and flanking region sequence and used the other TOR homolog and flanking region sequence to perform tBLASTx searches in the database (BLOSUM62 matrix; E-value = 1e-3; gap cost: existence 11, extension 1; and low complexity regions filter).

BLASTn was performed in CLC Bio main Workbench 6.0 with standard settings: "word size" 11, "match" 1, "mismatch" −3, "gap cost existence" 5, "gap cost extension" 2. Bowtie(26) was applied to perform the alignment of the reads to the reference genomes (see parameters in the script in Supporting Information).

BLAST analysis were performed using an expected threshold of 10, a word size of 11, a match/mismatch of 2-3 and gap cost existence of 5 and extension of 2. We only considered positive such sequences showing an e-value < 1E-20.

The General Search Parameters used were as follows: parameters automatically adjusted for short queries; maximum target sequences, 100; the E threshold was 10; word size, 3. The Scoring Algorithm Parameters were: matrix, BLOSUM62; gap costs, existence, 11 extension, 1; compositional adjustments, conditional compositional score matrix adjustment.

Default matrix parameters (BLOSUM62) and gap costs (Existence: 11 Extension: 1) were implemented, with an inclusion threshold of 0.005.

General parameters for similarity searches were: tblastx program, expect threshold value at 1.0e-50 1.0e-50g parameterscoringUM62 matrix; gaparametersxistence, 11; extension 1), and filter and masking, off.

Sequences without homology to known sequences were compared with less stringent settings to the available sequences in Genbank (expect threshold: 1000, Match/Mismatch Scores: 1.-1, Gap Costs: Existence: 2 Extension: 1), allowing more mismatches to occur in the comparison.

Discontinuous megablast: same parameters as those of similar sequence megablast with the exception word size, 11; match/mismatch scores, 2, -3; gap costs, existence: 5 extension: 2. The Swiss Institute of Bioinformatics SIB ExPASy Blast server [ 46] was used to find protein homologies.

Invisibility was the cost of existence.

EST and contig sequences were subjected to translated (blastx) searches against Arabidopsis proteins (TAIR9 annotation release [21]) with default settings, including: use of the BLOSUM62 matrix; expect threshold of 10; and, gap costs of existence: 11 and extension: 1.