ggsearch is part of the Fasta3 package, which contains many programs for searching DNA and protein databases as well as generating statistics for evaluating matches.

ggsearch compares a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using an algorithm based on the Needleman and Wunsch algorithm (Needleman and Wunsch, 1970). It calculates an alignment score that is global in the query and global in the library. ggsearch only compares the query to library sequences that are beween 80% and 125% of the length of the query.

In the Bio-Linux package, the threaded versions of the fasta programs are the default.

The programs available in the Fasta3 package are:

• fasta - scan a protein or DNA sequence library for similar sequences.
• fastx - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames.
• tfastx - compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations.
• fasty - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames.
• tfasty - compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations.
• fasts - compare unordered peptides to a protein sequence database
• tfasts - compare unordered peptides to a translated DNA sequence database
• fastm - compare ordered peptides (or short DNA sequences) to a protein (DNA) sequence database
• fastm - compare ordered peptides (or short DNA sequences) to a translated DNA sequence database
• fastf - compare mixed peptides to a protein sequence database
• tfastf - compare mixed peptides to a translated DNA sequence database
• ssearch - compare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm.
• ggsearch - compare a protein or DNA sequence to a sequence database using a global alignment (Needleman-Wunsch)
• lalign - produce multiple non-overlapping alignments for protein and DNA sequences using the Huang and Miller SIM algorithm for the Waterman-Eggert algorithm. This version of lalign replaces that from the Fasta2 package.
• prss - (discontinued, replaced in the fasta35 release by new versions of ssearch and fastx) estimate statistical significance of an alignment by comparing the score to the distribution of similarity scores generated by shuffling the second sequence. prss35 uses Smith-Waterman. prfx35 uses the fastx algorithm.

References:
Aaron J. Mackey, Timothy A. J. Haystead, and William R. Pearson. Algorithms for Rapid Protein Identification with Multiple Short Peptide Sequences. Mol Cell Proteomics 2002 1: 139-147 Full text

Pearson, W.R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol. 2000;132:185-219 [Entrez]

Pearson, W.R. Empirical statistical estimates for sequence similarity searches. J Mol Biol. 1998 Feb 13;276(1):71-84 [Entrez]

Pearson WR, Wood T, Zhang Z, Miller W. Comparison of DNA sequences with protein sequences. Genomics. 1997 Nov 15;46(1):24-36. [Entrez]