'extend a gap' is correct and usable in written English.
It is generally used to describe the action of making the space between two entities or points larger or widening the gap. For example, "The company took steps to extend the gap between their product and the competition."
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.
e i is the cost for extending a gap, where its value depends on whether i is within the seed region or not.
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).
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).
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.
Clustal W was performed by default: matrix was Gonnet 250; the penalty for opening a gap was 10; the penalty for extending a gap was 0.05; and gap separation penalty was 8. Secondary structures of the proteins were predicted by using the PSIPRED protein structure prediction server (PSIPRED v2.4 in ) [ 29].
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.
