2 AA Conservation version 1.0b (2 September 2010)
4 This program allows calculation of conservation of amino acids in
5 multiple sequence alignments.
6 It implements 17 different conservation scores as described by Valdar in
7 his paper (Scoring Residue Conservation, PROTEINS: Structure, Function
8 and Bioinformatics 48:227-241 (2002)) and SMERFS scoring algorithm as described
9 by Manning, Jefferson and Barton (The contrasting properties of conservation
10 and correlated phylogeny in protein functional residue prediction,
11 BMC Bioinformatics (2008)).
13 The conservation algorithms supported are:
15 KABAT, JORES, SCHNEIDER, SHENKIN, GERSTEIN, TAYLOR_GAPS, TAYLOR_NO_GAPS,
16 ZVELIBIL, KARLIN, ARMON, THOMPSON, NOT_LANCET, MIRNY, WILLIAMSON,
17 LANDGRAF, SANDER, VALDAR, SMERFS
19 Input format is either a FASTA formatted file containing aligned sequences with
20 gaps or a Clustal alignment. The valid gap characters are *, -, space character,
21 X and . (a dot). By default program prints the results to the command window.
22 If the output file is provided the results are printed to the file in two
23 possible formats with or without an alignment.
24 If format is not specified, the program outputs conservation scores without
25 alignment. The scores are not normalized by default but they can be (see below).
26 SMERFS default parameters are window width of 7, column score is set to
27 the middle column, gap% cutoff of 0.1. If different values for SMERFS parameters
28 are required than all three parameters must be provided. Details of the program
29 execution can be recorded to a separate file if an appropriate file path is
32 List of command line arguments:
34 -m= precedes a comma separated list of method names
35 EXAMPLE: -m=KABAT,JORES,GERSTEIN
36 Optional, if no method is specified request for all is assumed.
38 -i= precedes a full path to the input FASTA file, required
40 -o= precedes a full path to the output file, optional, if no output file is
41 provided the program will output to the standard out.
43 -t= precedes the number of CPUs (CPU cores more precisely) to use. Optional,
44 defaults to all processors available on the machine.
46 -f= precedes the format of the results in the output file
47 two different formats are possible:
50 Optional, if not specified RESULT_NO_ALIGNMENT is assumed
52 -s= precedes a list of three comma separated parameters for SMERFS
53 the order of parameters is as following:
54 1. window width - an integer and an odd number
55 2. how to allocate window scores to columns, two ways are possible:
56 MID_SCORE - gives the window score to the middle column
57 MAX_SCORE - gives the column the highest score of all the windows it
59 3. gap percentage cutoff - a float greater than 0 and smaller or equal 1
60 EXAMPLE: -s=5,MID_SCORE,0.1
61 Optional, default values are 7,MID_SCORE,0.1
63 -d= precedes a full path to a file where program execution details are to be
64 listed. Optional, if not provided, no execution statistics is produced.
66 -g= precedes comma separated list of gap characters provided by the user, if
67 you're using an unusual gap character (not a -,., ,*,X) you have to
68 provide it. If you you provide this list you have to list all the gaps
69 accepted. Including those that were previously treated as a default.
72 -n using this key causes the results to be normalized.
73 Normalized results have values between 0 and 1. Please note however, that
74 some results cannot be normalized. In such a case, the system returns not
75 normalized value, and log the issue to the standard error stream.
76 The following formula is used for normalization
77 n = (d - dmin)/(dmax - dmin)
78 Negative results first converted to positive by adding an absolute value of
79 the most negative result. Optional.
81 EXAMPLE HOW TO RUN THE PROGRAM:
82 java -jar <jar name> -m=KABAT,SMERFS -i=prot1 -o=prot1_results -n
84 As a result of the execution KABAT and SMERFS scores will be calculated.
85 Input comes form prot1 file and an output without an alignment is recorded to
88 Authors: Peter Troshin, Agnieszka Golicz, David Martin and Geoff Barton.
89 Please visit http://www.compbio.dundee.ac.uk for further information.