ALIGNMENT GLOBAL

 

Global sequence alignment

Program nameDescription
est2genome Align EST and genomic DNA sequences
needle Needleman-Wunsch global alignment
stretcher Finds the best global alignment between two sequences
alignrunner Runs alignment program on all sequence pairs in a directory
contactalign EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm
nawalign Damian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm
nawalignrunner Runs nawalign alignment program on all sequence pairs in a directory
needlerunner Runs needle alignment program on all sequence pairs in a directory
scorer Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment
scorerrunner Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third
substitute Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence)
substituterunner Runs substitute on directory of traces and writes substituted sequences to another
esim4 Align an mRNA to a genomic DNA sequence