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Sometimes one has several transformations and wants to combine them. For example, one may have transformations from an ALIGNFIT run (i.e. taken from a multiple alignment) and those from a STAMP run and want to combine them, since they have at least one domain in common. This would avoid having to run the more time-consumming STAMP program on things where similarity was obvious (i.e. clear sequence homologues). MERGETRANS allows this to be done.

The format is:

mergetrans -f1 <transformation file1> -f2 <transformation file2> [-i <domain identifier>]

If an identifier is given, then that identifier will be used to link the two files (provided it can be found in both). Otherwise the program will simply search for the first identifier that is exactly in common across the two transformation files.

One may also wish to extract particular transformations from a file. To do this, use EXTRANS as follows:

extrans -f <transformation file> -i <id1> <id2> <id3> ... <idN>

A new transformation file will be output to the standard output containing only those domains that have been input on the command line.

Geoff Barton