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[jabaws.git] / website / prog_docs / AACon_manual.txt

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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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