| ALIGNMENT GLOBAL

Global sequence alignment

Program name | Description
--- | ---
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