Sentence examples for extending a gap from inspiring English sources

e i is the cost for extending a gap, where its value depends on whether i is within the seed region or not.

PSI-BLAST computes and scores alignments using a heuristic approximation to the Smith Waterman algorithm (Smith and Waterman 1981) with affine gap costs (Gotoh 1982) providing uniform penalties for opening and extending a gap.

We used blast parameter values suitable for comparing divergent sequences (word size = 7; match score = +1; mismatch score = -1; initial penalty for opening a gap = 1; penalty for extending a gap = 2).

Alignments of the nine sub-gene families were manually curated after aligning them with MACSE [ 33], allowing stop codons and introducing penalties for creation of a gap (-7), extending a gap (-1), and introducing frameshift (-14).

Subsequently, the sequence databases of the National Center for Biotechnology Information (NCBI) [ 51] were searched for homologous protein sequences using tBLASTx with an expect threshold of 10, a word size of 3, gap costs of 11 for opening a gap, and gap costs of 1 for extending a gap (filtering disabled).

The sequences of each subset were aligned using ClustalW [ 39]: various protein comparison matrix (e.g., Gonnet, Blosum and PAM) were tested and for each type of matrix, various combinations of the parameter values (i.e., the penalty for opening, closing, extending a gap and for the gap separation) were used.

The score to extend a gap along the genome sequence was set at −2 and the score to extend a gap along the read sequence was set at −1.

The parameters were set to: amino acid substitution matrix BLOSUM62, a statistical significance threshold of 10 for similarity matches, and costs to open an alignment gap and extend a gap of 11 and 1, respectively.

Blastx parameters were set to: amino acid substitution matrix BLOSUM-62 [ 75], a statistical significance threshold of 10 for database matches [ 76] and costs to open an alignment gap and extend a gap of 11 and 1 respectively.

Further settings were chosen as follows: cost to open a gap = 25, cost to extend a gap = 10, reward for a nucleotide match = 2, penalty for a nucleotide mismatch = -3, word size = 56, megablast search = T, number of alignments to show = 1.

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