English
资源说明：A new ESST generator
= ulla
http://www-cryst.bioc.cam.ac.uk/ulla
== Description
'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.
== Features
* Environment-specific substitution table generation based on user providing environmental class definition
* Entropy-based smoothing procedures to cope with sparse data problem
* BLOSUM-like weighting procedures using PID threshold
* Heat Map generation for substitution tables
== Requirements
* ruby 1.8.7 or above (1.9.0 or above recommended, http://www.ruby-lang.org)
* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems)
Following RubyGems will be automatically installed if you have rubygems installed on your machine
* narray (http://narray.rubyforge.org)
* bio (http://bioruby.open-bio.org)
* RMagick (http://rmagick.rubyforge.org)
== Installation
~user $ sudo gem install ulla
== Basic Usage
It's pretty much the same as Kenji's subst (http://mordred.bioc.cam.ac.uk/~kenji/subst/), so in most cases, you can swap 'subst' with 'ulla'.
~user $ ulla -l TEMLIST-file -c classdef.dat
or
~user $ ulla -f TEM-file -c classdef.dat
== Options
--tem-file (-f) FILE: a tem file
--tem-list (-l) FILE: a list for tem files
--classdef (-c) FILE: a file for the defintion of environmental class
if no definition file provided, --cys (-y) 2 and --nosmooth options automatcially applied
--outfile (-o) FILE: output filename (default 'allmat.dat')
--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
--noweight: calculate substitution counts with no weights
--environment (-e) INTEGER:
0 for considering only substituted amino acids' environments (default)
1 for considering both substituted and substituting amino acids' environments
--smooth (-s) INTEGER:
0 for partial smoothing (default)
1 for full smoothing
--p1smooth: perform smoothing for p1 probability calculation when partial smoothing
--nosmooth: perform no smoothing operation
--cys (-y) INTEGER:
0 for using C and J only for structure (default)
1 for both structure and sequence
2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
--output INTEGER:
0 for raw counts (no smoothing performed)
1 for probabilities
2 for log-odds (default)
--noroundoff: do not round off log odds ratio
--scale INTEGER: log-odds matrices in 1/n bit units (default 3)
--sigma DOUBLE: change the sigma value for smoothing (default 5.0)
--autosigma: automatically adjust the sigma value for smoothing
--add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 0)
--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
--heatmap INTEGER:
0 create a heat map file for each substitution table
1 create one big file containing all heat maps from substitution tables
2 do both 0 and 1
--heatmap-format INTEGER:
0 for Portable Network Graphics (PNG) Format (default)
1 for Graphics Interchange Format (GIF)
2 for Joint Photographic Experts Group (JPEG) Format
3 for Microsoft Windows bitmap (BMP) Format
4 for Portable Document Format (PDF)
--heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
--heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
--heatmap-values: print values in the cells when generating heat maps
--verbose (-v) INTEGER
0 for ERROR level
1 for WARN or above level (default)
2 for INFO or above level
3 for DEBUG or above level
--version: print version
--help (-h): show help
== Usage
1. Prepare an environmental class definition file. For more details, please check this notes (http://mordred.bioc.cam.ac.uk/~kenji/subst/NOTES). You can download a sample environmental class definition file from http://mordred.bioc.cam.ac.uk/~kenji/subst/classdef.dat
~user $ cat classdef.dat
#
# name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
# constrained or not (T or F); silent (used as masks)? (T or F)
#
secondary structure and phi angle;HEPC;HEPC;T;F
solvent accessibility;TF;Aa;F;F
2. Prepare structural alignments and their annotations of above environmental classes in PIR format. You can download sample alignments from http://mordred.bioc.cam.ac.uk/~kenji/subst/alltem-allmask.tar.gz or from http://www-cryst.bioc.cam.ac.uk/ESST/
~user $ cat sample1.tem
>P1;1mnma
sequence
QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
IQACLNAPDD*
>P1;1egwa
sequence
--GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
----------*
>P1;1mnma
secondary structure and phi angle
CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
HHHHHCCCCP*
>P1;1egwa
secondary structure and phi angle
--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
----------*
>P1;1mnma
solvent accessibility
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
TTTTTTTTTT*
>P1;1egwa
solvent accessibility
--TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
----------*
...
3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
~user $ ls -1 *.tem > TEMLIST
~user $ cat TEMLIST
sample1.tem
sample2.tem
...
4. To produce substitution count matrices,
~user $ ulla -l TEMLIST --output 0 -o substcount.mat
5. To produce substitution probability matrices,
~user $ ulla -l TEMLIST --output 1 -o substprob.mat
6. To produce log odds ratio matrices,
~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
7. To produce substitution probability matrices from the sequence pairs within a certain PID range (if you don't provide any name for output, 'allmat.dat' will be used.),
~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
8. To change the clustering level (default 60) to PID 80,
~user $ ulla -l TEMLIST --weight 80 --output 1
9. In case positions are masked with the character 'X' in any environmental features, all mutations from/to the position will be excluded from substitution counts.
10. Then, it will produce a file containing all the matrices, which will look like the one below. For more details, please check this notes (http://mordred.bioc.cam.ac.uk/~kenji/subst/NOTES).
# Environment-specific amino acid substitution matrices
# Creator: ulla version 0.0.5
# Creation Date: 05/02/2009 17:29
#
# Definitions for structural environments:
# 2 features used
#
# secondary structure and phi angle;HEPC;HEPC;F;F
# solvent accessibility;TF;Aa;F;F
# (read in from classdef.dat)
#
# Number of alignments: 1187
# (list of .tem files read in from TEMLIST)
#
# Total number of environments: 8
#
# There are 21 amino acids considered.
# ACDEFGHIKLMNPQRSTVWYJ
#
# C: Cystine (the disulfide-bonded form)
# J: Cysteine (the free thiol form)
#
# Weighting scheme: clustering at PID 60 level
# ...
#
>HA 0
# A C D E F G H I K L M N P Q R S T V W Y J
A 3 -5 0 0 -1 2 0 0 1 0 0 0 1 1 0 1 1 1 -1 0 2
C -16 19 -16 -18 -11 -14 -13 -13 -14 -14 -14 -11 -17 -16 -13 -16 -14 -12 -12 -10 -4
D 1 -7 6 3 -3 1 0 -3 1 -3 -2 2 1 2 0 1 0 -2 -3 -2 -2
E 3 -7 5 7 -1 2 2 0 3 0 0 3 2 4 3 3 2 1 -1 0 -1
F -4 -4 -6 -6 7 -5 -1 0 -4 1 0 -5 -5 -4 -4 -4 -3 -1 3 3 0
G -2 -6 -3 -4 -5 5 -4 -5 -4 -5 -4 -2 -3 -4 -4 -2 -3 -5 -6 -4 -3
H 0 -6 0 0 1 0 8 -1 0 0 0 1 -2 1 1 0 0 0 1 3 0
I -3 -7 -6 -5 0 -5 -3 4 -4 1 1 -5 -4 -4 -3 -5 -2 2 -2 -1 0
K 2 -6 2 2 -1 1 2 0 5 1 1 2 0 3 4 2 2 0 -2 0 -1
L -2 -6 -5 -4 1 -4 -2 2 -3 4 2 -3 -4 -3 -2 -4 -2 1 0 0 1
M -2 -7 -4 -3 1 -2 -1 2 -2 2 6 -3 -4 -2 -1 -2 -1 1 0 0 1
N 0 -5 1 0 -3 1 1 -3 0 -2 -2 6 -2 0 0 1 1 -2 -3 -1 -1
P -1 -7 -1 -2 -4 -1 -3 -3 -2 -3 -4 -2 9 -2 -3 0 -1 -2 -4 -4 -4
Q 2 -7 2 2 -1 1 2 -1 2 0 0 2 0 5 2 1 1 0 -2 -1 0
R 1 -6 1 1 -1 0 2 0 3 0 1 1 -1 2 6 1 1 0 -1 0 0
S 0 -6 -1 -1 -3 0 -2 -3 -1 -3 -3 0 0 -1 -1 3 1 -2 -4 -3 0
T -1 -7 -2 -2 -3 -2 -2 -2 -2 -2 -2 -1 -2 -2 -2 0 3 -1 -3 -3 0
V -3 -6 -6 -5 -1 -4 -3 1 -4 0 0 -5 -3 -4 -4 -4 -2 2 -2 -2 0
W -4 -6 -6 -5 2 -6 -2 -2 -5 -1 -2 -5 -5 -4 -4 -5 -4 -2 12 2 -3
Y -3 -5 -5 -5 3 -4 1 -1 -3 -1 -1 -3 -5 -3 -3 -4 -3 -2 3 7 -1
J -2 0 -4 -5 0 -2 -1 0 -3 0 0 -3 -6 -2 -2 -1 -1 0 -1 0 9
U -5 16 -7 -8 -3 -5 -4 -3 -6 -3 -3 -5 -9 -6 -5 -4 -4 -3 -4 -3 6
...
11. To generate a heat map for each table with values in it,
~user $ ulla -l TEMLIST --heatmap 0 --heatmap-values
which will look like this,
http://mordred.bioc.cam.ac.uk/~semin/images/0.HA.png
12. To generate one big figure, 'myheatmaps.gif' containing all the heat maps (4 maps in a row),
~user $ ulla -l TEMLIST --heatmap 1 --heatmap-stem myheatmaps --heatmap-format 1 --heatmap-columns 4
which will look like this,
http://mordred.bioc.cam.ac.uk/~semin/images/myheatmaps.gif
== Repository
You can download a pre-built RubyGems package from
* rubyforge: http://rubyforge.org/projects/ulla
or, You can fetch the source from
* github: http://github.com/semin/ulla/tree/master
== Reference
* {Lee S., Blundell T.L. (2009) Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinformatics. 25(15):1976-1977; doi:10.1093/bioinformatics/btp300}[http://bioinformatics.oxfordjournals.org/cgi/content/full/25/15/1976]
== Contact
Comments are welcome, please send an email to me (seminlee at gmail dot com).
== License
http://i.creativecommons.org/l/by-nc/2.0/uk/88x31.png
This work is licensed under a {Creative Commons Attribution-Noncommercial 2.0 UK: England & Wales License}[http://creativecommons.org/licenses/by-nc/2.0/uk/].
本源码包内暂不包含可直接显示的源代码文件，请下载源码包。
