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Description of the AMPS package

Version D2.0 consists of the following programs.

MULTALIGN (AMULT/FSCAN) performs a number of functions. These include pairwise sequence alignment and assessment of statistical significance, multiple alignment by the methods of Barton and Sternberg (1987b) and a method similar to that of Feng and Doolittle (1987), and additional functions that allow the inclusion of variable gap-penalties and specific weighting schemes. Each aspect of this program and its use is described below.

ORDER uses the output from a MULTALIGN pairwise run to perform cluster analysis (tree generation), ordering of the sequences by similarity and general format changes.

DAYB takes a sequence in seq_file format and creates a file in block_file format. Just type DAYB and follow the instructions.

SORTER takes the output of a database scan and sorts the results into descending-score order. SORTER also allows construction of histograms and extraction of the identifying codes for the top scoring proteins.

SELECT takes a list of protein identifier codes and a sequence database and extracts the sequences from the database that correspond to the codes. Unlike some programs (e.g. PSQ) the sequences are output in the same order as the codes are presented. SELECT is normally used in conjunction with SORTER.

PATT Processes the output of a flexible pattern analysis to produce a more readable output.