Table 1

GATAligner parameters and features

NCBI-BLASTN Parameters

Nucleotide Match

Score added to the total for each match.

Nucleotide Mismatch

Score subtracted from total for each mismatch.

Gap Creation

Score subtracted from total for each new gap.

Gap Extension

Score subtracted from total for each additional base in a gap after its creation.

Low Complexity Mask

Use of DUST to mask and thus not align regions of low complexity.

GATAligner Parameters

Window Size

Size of window used to score sub-alignments in each local alignment. Sub-alignments smaller than the window size will be saved provided they are at or above the score cut off. When aligning longer sequences, increase the size of the window as well as the cut off score to minimize non-related alignments.

Score Cut Off

Score (raw or bits) at which windowed sub-alignments are saved or discarded. The higher this score is set the faster GATAligner will run. Set between 20–25 bits for a window size of 24 when aligning sequences less than 10 KB. For larger sequences, increase the cut off and window size (e.g. 30 bits and 30 bp).

Start Positions for Reference and Comparative Sequences

Use this to maintain register with gene annotation.


GATAligner is multithreaded. Queue up multiple alignments.

Nix and Eisen BMC Bioinformatics 2005 6:9   doi:10.1186/1471-2105-6-9

Open Data