Consensus Server 2

Consensus Server 2.3

AUTHOR

Jay H. Choi

jhc1@genetics.wustl.edu

http://www.cmpharm.ucsf.edu/~jchoi

ABSTRACT

This is a consensus server with a web-based graphic interface for motif pattern search program, consensus; consensus, wconsensus, & consensus-vio. It contains cgi module, graphic module, processing module to let user run motif search software and create a web-based graphic result interactively. Features include:

1. Web-based user interface of consensus, wconsensus & consensus-vio.

2. Graphical representation of search result.

3. Sequence logo of output motif pattern.

4. Sequence graph of output motif pattern against input sequence.

5. Sequence with highlight regions based on motifs found from search.

6. Repeating motif search excluding pattern found in previous runs.

For full information on usage, see the accompanying html documentation.

SYSTEM REQUIREMENTS

1. Platform : Sun Solaris Sparc 2.6 & Red Hat Linux 6.2 (or higher version)

2. Web Browser: Netscape 6, Mozilla 5.0, Konqueror 3.0, Internet Explorer 5.0 (or higher version)

3. Perl Module (Perl 5.06 or higher): GD-2.07 & GDGraph-1.39

4. Image Tool: ImageMagick 5.4.3

5. HTTP Server: Apache 1.3.2 (or higher version)

6. Compiler: Gnu C Compiler, gcc version 2.8.1 or higher.

* Older versions may work without any problems; however they are only

tested with listed versions.

CONSENSUS GRAPHIC INTERFACE (version 2.3)

This is an interactive graphic user interface of consensus application package. This program lets users run consensus software and generate various types of graphical outputs for result analysis. The server is designed to prompts the user for email submission option if the input query sequence is too large. If the email option is chosen, the server will take the query, and email the output as soon as the search process is done. (see Consensus Graphic Viewer for loading the output for graphical analysis).

1. Sequence File: a sequence formats that consensus server v2.3 takes are FASTA or CONSENSUS format. (see consensus, consensus-vio, or wconsensus) for more detailed information. Originally, the space in the name of sequence is now allowed in consensus applications. In consensus server, it will replace the space with ‘_’ character to avoid the software error or unexpected problems.

2. Motif Pattern Length: this will determine the length of consensus motif pattern you are searching for. For a fast search method (see below), if the length is provided by the user, consensus-vio will perform the search with –l option. Otherwise, it will perform a dynamic with search (see consensus-vio documentation). For an exhaustive search method, if the length is provided, consensus-v6c will be used for search (see consensus documentation). Otherwise, wconsensus will be used for unknown width search (see wconsensus documentation).

3. Search Method: there are two search methods available. Fast search method uses consensus-vio (consensus – version of iteration optimization). Consensus-vio obtains an initial pattern matrix by linear runs of consensus-v6c or wconsensus-v5c, and enhances the pattern matrix thru cycles of optimization steps. (see consensus-vio documentation). Exhaustive method uses consensus-v6c & wconsensus-v5c to search for the statistically most significant & probable pattern matrix determined by the expected frequency of the matrix alignment.

4. Sequence Alphabet: only DNA and protein sequence alphabet can be used for a motif search thru consensus server.

5. Complement: for DNA sequence, two types of complement options can be chosen by the user. If c1 option is chosen, the search treats both positive and negative strands as separate sequences; thus, it will double the number of sequences. If c1 option is chosen, the search will treat them as a single sequence by appending the negative sequence to the positive sequence; thus the length of sequence will be double during the search.

6. Alphabet Prior Frequency: the user has an option to provide a prior frequency of alphabet for an input sequence set. If the prior frequency is not provided, then the observed frequency from the input sequence will be used in the search process.

CONSENSUS GRAPHIC VIEWER (VERSION 1.2)

This is an interactive graphic viewer of consensus application package. This will let users load the consensus text format based output, and generate the graphic based output to analyze the result.

1. Result File: a result file should be a non-modified text format result from consensus-v6c, consensus-vio, or wconsensus-v5c.

2. Sequence File: a sequence file should be the exactly same input sequence file you used for a search to obtain the result file. Providing the different sequence file will cause the unexpected error.

CONSENSUS RERUN SEARCH

This is a method lets users to run consensus application again to search for more consensus motifs beside ones you have found from the previous search. The search procedure excludes the regions of sequences that makes up the previous motif pattern during the search process, and outputs the motif pattern matrix that were not found from the previous search. This process can be repeated more than once to iteratively find multiple consensus motifs in a sequence set.

CONSENSUS SEQUENCE GRAPH

The sequence graph is a graphical representation of sequence with score bars and lines based on a particular motif pattern scoring against input sequence. The motif pattern matrix will be scanned against the input sequence, and each position of sequences will get the score. The positions that scores higher than a cutoff score (statistically significant value calculated based on a length & number of sequence, and width of pattern matrix) will be represented as a bar. The height of a bar represents the score of particular position in the sequence. The line represents also represents the score of each position.

1. Title Option: a title of sequence graph. It will be embedded in the sequence graph image.

2. Label Option: this option will set the anchor point and its position number. For example, if set an anchor point to a lower bound at 0, the sequence graph will starts from 0. If the anchor point is set to a upper bound at 0, the sequence graph starts from –length of sequence to 0.

3. Legend & Value Option:

i. Show Legend: it will show the legend of each motif.

ii. Show Color Table: a color table with a range of score values will be shown upper left corner of sequence graph.

iii. Show Data Value: data value of each motif will be shown on top of bar.

4. Gridline Option: major gridline will dissects the sequence graph line into 6 divisions. Minor gridline will dissects into 3.

5. Drawing Option:

i. Show Only Starting Position: a bar representing the high scoring motif (scored above cutoff score) will be shown at the starting position of motif pattern. The height will represent the score of motif patter against the sequence.

ii. Show Full Length of Pattern: rectangular box that starts from the starting position to end position of pattern motif will be shown. The height will represent the score, and width will represents the length of motif pattern.

CONSENSUS SEQUENCE LOGO

The sequence logo was originally developed by Thomas D. Schneider. This is a modified version of sequence logo exclusively used for consensus motif pattern. All copyrights goes to Thomas D. Schneider.

1. Title Option: it will let users to put a title in a sequence logo image. X & Y position locates the upper left corner of starting position of title. Size will determine the size of font used in a title.

2. Layout Option: four coordinate numbers will determine where the sequence logo image will be located. They are indent values for a sequence logo image.

3. Display Option:

i. Position Number: sequence position number displayed on the x-axis.

ii. Letter Outlines: if chosen, the letter will be drawn with an outline.

iii. Y-axis: if checked, y-axis will be shown on the image.

iv. Boxed Character: if checked, the letter will be put in a box.

4. Advanced Layout Option:

i. Width of Character: width of a single letter in a sequence logo image.

ii. Width of Vertical Bars: width of y-axis.

iii. Height of Vertical Bars (cm): height of y-axis.

iv. Height of Vertical Bars (bits): number of bits to represent sequence logo letter.

v. Boxed Character Shrinking Factor: character-shrinking factor inside box.

vi. Rotation Angle of Logo: angle to rotate the sequence logo image.

COPYRIGHT INFORMATION

used in Consensus Server are copyrighted separately by its author.

THE LATEST VERSION

ConsensusServer 2.3

INSTALLATION

Read these instructions all the way through before you start!

1. Make sure you have downloaded and installed the following packages:

a. Perl 5.004 or higher:

http://www.perl.com

b. GD 2.0.7 & GDGraph-1.39

http://www.cpan.org

c. ImageMagick 5.4.3 or higher:

http://www.iamgemagick.org

d. Apache HTTP Server: 1.3.2 or higher.

http://httpd.apache.org

NOTE: GD & GDGraph modules have requirements for their installation.

See for their installation guide.

2. Unpack the tar file:

tar -zxvf ConsensusServer-2.0.tar.gz

zcat ConsensusServer-2.0.tar.gz | tar xvf -

* This will create the directory consensus.

3. To install Consensus Server on a system:

a. cd consensus

b edit config file. (see the instruction in config file)

c. make install

* This will compile & install all the softwares required

by Consensus Server.

4. To uninstall Consensus Server on a system.

a. cd consensus.

b. make uninstall.

* This will remove all object files of softwares and remove current

configuration.

IF YOU RUN INTO PROBLEMS

FREQUENTLY ASKED QUESTIONS

SECURITY & CONFIGURATION OF SERVER

In general, web servers are large, complex programs that can contain security holes in your system. The open architecture of web servers allows arbitrary CGI scripts to be executed on the server's side of the connection in response to remote requests. Any CGI script installed at your site may contain bugs, and every such bug is a potential security hole. Thus, CGI scripts are a major source of security holes. Unfortunately, the consensus server package was not developed with much care on security issues. Therefore, before you install this package, you should consult you Network administrator if you plan to make this server available to the public. You should also consult your administrator about the HTTP-server configuration of 'cgi-bin' directory. Depends on its configuration, the server can be accessible from the public or local network. For more information about the security issues, go to http://www.w3.org/Security.

BUG REPORTS

Feel free to contact me via e-mail, subject to the caveats below. Provide the version numbers of Perl, and Perl module, make and model of your operating system, and make and model of your Web server and Web browser. Provide a small script that demonstrates the bug.

Do NOT contact me for issues involving compilation failures on Windows, VMS, or Macintosh systems. I do not have any such systems on hand, and cannot help you out.

Also do NOT contact me for issues involving the Netscape 4.0 or lower, Internet Explorer 4.0 or lower, Mozilla 4.0 or lower, and Konquerer 2.0 or lower versions of web browser. Also, I cannot help you with problems involved other web browsers.

ACKNOWLEDGEMENTS

I would like to thank Junghei Julie Kim for her contribution to the fundamental design of server, and for her support and encouragement throughout the time.

UPDATES

The current version of Consensus Server can be found in http://stemloop.wustl.edu/consensus/html/Html/download.html