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-
-AA Conservation version 1.0b (2 September 2010)
-
-This program allows calculation of conservation of amino acids in
-multiple sequence alignments.
-It implements 17 different conservation scores as described by Valdar in
-his paper (Scoring Residue Conservation, PROTEINS: Structure, Function
-and Bioinformatics 48:227-241 (2002)) and SMERFS scoring algorithm as described
-by Manning, Jefferson and Barton (The contrasting properties of conservation
-and correlated phylogeny in protein functional residue prediction,
-BMC Bioinformatics (2008)).
-
-The conservation algorithms supported are:
-
-KABAT, JORES, SCHNEIDER, SHENKIN, GERSTEIN, TAYLOR_GAPS, TAYLOR_NO_GAPS,
-ZVELIBIL, KARLIN, ARMON, THOMPSON, NOT_LANCET, MIRNY, WILLIAMSON,
-LANDGRAF, SANDER, VALDAR, SMERFS
-
-Input format is either a FASTA formatted file containing aligned sequences with
-gaps or a Clustal alignment. The valid gap characters are *, -, space character,
-X and . (a dot). By default program prints the results to the command window.
-If the output file is provided the results are printed to the file in two
-possible formats with or without an alignment.
-If format is not specified, the program outputs conservation scores without
-alignment. The scores are not normalized by default but they can be (see below).
-SMERFS default parameters are window width of 7, column score is set to
-the middle column (MID_SCORE), gap% cutoff of 0.1. Different parameters for SMERFS
-can be provided (see below). Details of the program execution can be recorded to
-a separate file if an appropriate file path is provided.
-
-List of command line arguments:
-
--m= precedes a comma separated list of method names
- EXAMPLE: -m=KABAT,JORES,GERSTEIN
- Optional, if no method is specified request for all is assumed.
-
--i= precedes a full path to the input FASTA file, required
-
--o= precedes a full path to the output file, optional, if no output file is
- provided the program will output to the standard out.
-
--t= precedes the number of CPUs (CPU cores more precisely) to use. Optional,
- defaults to all processors available on the machine.
-
--f= precedes the format of the results in the output file
- two different formats are possible:
- RESULT_WITH_ALIGNMENT
- RESULT_NO_ALIGNMENT
- Optional, if not specified RESULT_NO_ALIGNMENT is assumed
-
--d= precedes a full path to a file where program execution details are to be
- listed. Optional, if not provided, no execution statistics is produced.
-
--g= precedes comma separated list of gap characters provided by the user, if
- you're using an unusual gap character (not a -,., ,*,X) you have to
- provide it. If you you provide this list you have to list all the gaps
- accepted. Including those that were previously treated as a default.
- Optional.
-
--n using this key causes the results to be normalized.
- Normalized results have values between 0 and 1. Please note however, that
- some results cannot be normalized. In such a case, the system returns not
- normalized value, and log the issue to the standard error stream.
- The following formula is used for normalization
- n = (d - dmin)/(dmax - dmin)
- Negative results first converted to positive by adding an absolute value of
- the most negative result. Optional.
-
-SMERFS Only Parameters:
-
--smerfsGT= precedes SMERFS Gap Treshold - a gap percentage cutoff -
- a float greater than 0 and smaller or equal 1. Optional defaults
- to 0.1
-
--smerfsCS= precedes SMERFS Column Score algorithm defines the window scores to
- columns allocation , two methods are possible:
- MID_SCORE - gives the window score to the middle column
- MAX_SCORE - gives the column the highest score of all the windows it
- belongs to. Optional defaults to MID_SCORE.
-
--smerfsWW= precedes Window Width parameter - an integer and an odd number.
- Optional, defaults to 7
-
-
-EXAMPLE HOW TO RUN THE PROGRAM:
-java -jar <jar name> -m=KABAT,SMERFS -i=prot1 -o=prot1_results -n
-
-As a result of the execution KABAT and SMERFS scores will be calculated.
-Input comes form prot1 file and an output without an alignment is recorded to
-prot1_results file.
-
-Authors: Peter Troshin, Agnieszka Golicz, David Martin and Geoff Barton.
-Please visit http://www.compbio.dundee.ac.uk/aacon for further information.
-
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