Recent Posts

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71
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by xiangjun on September 26, 2016, 11:18:16 pm »
Hi Kate,

Yes. You need to edit file $REDUCE_SUITE/html/LogoGenerator_PS.def slightly, as shown below.

Current (default settings):
Code: [Select]
/colorDict <<
    (A) green       (a) m_green
    (C) blue        (c) m_blue
    (G) orange      (g) m_orange
    (T) red         (t) m_red
    (U) cyan        (u) m_cyan
    (X) white
>> def

Change (U) cyan to (U) red will achieve what you asked. Of course, you can completely redefine the coloring scheme as you see fit in section "default color set".

A bit background info for the default colors: the A green, C blue, G orange, and T red coloring scheme follows WebLogo for DNA. On the other hand, the 3DNA software for 3D structures of DNA/RNA uses another convention: A red, C yellow, G green, T blue, and U cyan. See http://x3dna.org/articles/seeing-is-understanding-as-well-as-believing for some examples. So I ended up with cyan for U in RNA logo. Moreover, the REDUCE Suite Forum is based on the 3DNA Forum.

Best regards,

Xiang-Jun
72
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 26, 2016, 06:03:44 pm »
Hi Xiang-Jun,

As a followup question:
The default color of the nucleotide "U" from `LogoGenerator -rna` is light blue. Is it possible to change it to red (like the color of "T" in DNA logos)?

Best,
Kate
73
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 22, 2016, 03:31:21 pm »
Hi Xiangjun,

Perfect! Many thanks for the prompt reply.

Best,
Kate
74
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by xiangjun on September 22, 2016, 10:29:37 am »
Hi Kate,

Thanks for using the REDUCE Suite and for posting your question on the Forum.

Yes, LogoGenerator is applicable to RNA as well as DNA. You just need to specify an additional -rna option on the command-line, and everything else should work as expected. Please have a try and report back any issues you may have.

Best regards,

Xiang-Jun


PS. The REDUCE Suite has more features than those documented (with the command-line "-h" option). The default settings are designed to work for its advertised purpose only.
75
General Discussion / Generate RNA logos with LogoGenerator
« Last post by knie on September 22, 2016, 06:36:17 am »
Hi,

Is it possible to generate RNA logos with LogoGenerator? (i.e., display U instead of T)

TIA.
Kate
76
General Discussion / Re: Defining Color in LogoGenerator
« Last post by xiangjun on August 11, 2016, 01:40:58 pm »
Hi,

Thanks for being the first to ask questions on the Forum! I'd like to clarify that the LogoGenerator utility is within the REDUCE Suite, which is a completely separate package from FeatureReduce.

As to your question of coloring some Cs (or other bases) in separately color, the answer is no, at least in the current version of LogoGenerator. The DNA/RNA logos, as I am aware of, consist of 4 different bases, as shown in the 4 columns of a PWM or PSAM. To color certain bases differently, such info must be specified in some way in the file, which will break the format.

There are so many logo generators available. Maybe some of them are more advanced than the functionality LogoGenerator currently provides, and can do what you are asking for.

If you want to generate only a fews logos, you could use LogoGenerator to generate the logos in EPS format. Then using Adobe Illustrator, you can edit/modify as you see fit.

Hope this helps.

Xiang-Jun

77
General Discussion / Defining Color in LogoGenerator
« Last post by jukri on August 11, 2016, 01:25:08 pm »
Is it possible to add a color feature for the LogoGenerator function in FeatureReduce? I would like to e.g have a C nucleotide colored in different shades of blue, depending on the experimental condition it came from?

Thanks
78
Documentation / LogoGenerator
« Last post by xiangjun on July 29, 2016, 04:20:35 pm »
The LogoGenerator utility program in the REDUCE Suite is a versatile and robust command-line tool that generates logo images in a variety of styles (raw data, frequency, conventional bit information, or affinity logo in ΔΔG). The input can be either a PSAM, or other common formats (such as a PWM, a multiple sequence alignment file in either FASTA or flat format) converted to a pseudo-PSAM via the utility program Convert2PSAM. The output logo image is in EPS format and is converted to PNG format by default for display in a web page (as from HTMLSummary), using the widely and freely available tool GhostScript tool gs. Other supported image formats include PDF, JPEG, and GIF (further utilizing the convert utility program from ImageMagick).

LogoGenerator [options] -file=PSAM_File

  Required parameters:
    -file=PSAM_file     --- name of the PSAM matrix file to get a logo

  Optional parameters:
    [-output=dir_name]  --- path to the output directory (./)
    [-logo=IMAGE_file]  --- name of output logo image file (base-filename.png)
    [-format=IMAGE_FMT] --- image format of the logo: eps|pdf|jpeg|png (png)
                            Note: o pdf, jpeg and png formats make use of "gs",
                                  o check 'pkg_settings.cfg' for settings
    [-style=LOGO_STYLE] --- style of the logo: raw|freq|bits_info|ddG (bits_info)
    [-type=INPUT_TYPE]  --- input type for generating the logo: PSAM|fasta|flat
                            If in 'fasta' or 'flat' format, the sequences must be
                            already aligned and of the same length (PSAM)
    [-title=string]     --- title string of the logo image
    [-width=float]      --- logo width in cm (12)
    [-height=float]     --- logo height in cm (7.5)
    [-ymin=float]       --- minimum value on the y-axis
    [-ymax=float]       --- maximum value on the y-axis
    [-frame]            --- switch for drawing a bounding box around the logo
    [-bw]               --- switch for black-and-white the logo image
    [-reverse_comp]     --- draw logo based on reverse complementary strand
    [-rna]              --- draw RNA logo (i.e., using U instead of T)

  Usage:
      LogoGenerator -file=$REDUCE_SUITE/data/formats/psam_ex.dat -logo=sample.png

  Note:
      For non-PSAM file formats (e.g., PWM), please see 'Convert2PSAM'
79
Documentation / Summary of the REDUCE Suite v2.2 programs
« Last post by xiangjun on July 29, 2016, 04:08:51 pm »
The REDUCE Suite v2.2 contains a total of 12 programs, as outlined below. The software is distributed with full source code in ANSI C. For the benefit of users, precompiled binaries for the most common Linux, Mac OS X, and Windows operating systems are also provided. Command-line help message is available for each program by specifying the -h option (e.g., LogoGenerator -h), which also include sample usages to get you started. If you have any questions in using the Suite, please do not hesitate to post them on the Forum.

Motif discovery and model building:

  • MotifREDUCE — An algorithm that builds a motif-based multivariate linear model. REDUCE is an acronym that stands for Regulatory Element Detection Using Correlation with Expression. Based on a simple model for transcriptional regulation by independently acting transcription factors (Bussemaker et al, 2001), REDUCE makes it possible to discover regulatory motifs based on a single microarray experiment. MotifREDUCE is a robust and efficient reimplementation of the original REDUCE algorithm. Required inputs are (i) a genome-wide set of measurements (mRNA expression log-ratios or ChIP fold-enrichments) and (ii) a nucleotide sequence associated with each measurement (e.g., upstream promoter sequence). Output are (i) a set of cis-regulatory oligonucleotide motifs, and (ii) the corresponding regression coefficients.
  • MatrixREDUCE — A more sophisticated algorithm that builds a multivariate linear model based on weight matrices (Foat et al., 2005, 2006). Required inputs are the same as far MotifREDUCE: (i) a genome-wide set of measurements (mRNA expression log-ratios or ChIP fold-enrichments) and (ii) a nucleotide sequence associated with each measurement (e.g., upstream promoter sequence). Outputs include (i) the binding specificity, in the form of a position-specific affinity matrix (PSAM), and (ii) the condition-specific concentration/activity for each of a set of trans-acting factors (TF).
  • OptimizePSAM — Fits PSAM parameters and coefficients for a single-TF model. MatrixREDUCE makes iterative calls to this program to build a multivariate model.
  • Transfactivity — Fit a multivariate linear model to one or more genome-wide sets of measurements. In contrast to MotifREDUCE/MatrixREDUCE, motifs/PSAMs are not inferred from the data, as in, but instead are provided as inputs. This is useful for inferring changes in the (hidden) regulatory activity of one or more TFs of known binding specificity. Transfactivity is a contraction of "trans-factor" and "activity".

Visualization of results:
  • HTMLSummary — A utility for visualizing the result of a MatrixREDUCE or MotifREDUCE run in HTML format.
  • LogoGenerator — A versatile and robust command-line tool that generates logo images in a variety of styles (raw data, frequency, conventional bit information, or affinity logo in ??G). The input can be a PSAM or a multiple sequence alignment file in either FASTA or flat format. The output logo image is in EPS format and is converted to PNG format by default for display in a web page (as from HTMLSummary), using the widely and freely available tool GhostScript tool gs. Other supported image formats include PDF, JPEG, and GIF (further utilizing the convert utility program from ImageMagick).

Affinity-based sequence analysis:
  • AffinityProfile — Convert one or more DNA/RNA sequences to single-nucleotide resolution affinity profiles or a total regional affinity. A set of motifs and/or PSAMs is required as input.

Miscellaneous utilities:
  • Convert2PSAM — Convert commonly used motif (pattern) representations of nucleic acid sequences to PSAM format, which is unique to the REDUCE Suite. It also serves to standardize the various formats to a simplified PWM format for easy communication.
  • Topo2Dictfile — Generate a motif dictionary file according to user-specified topological patterns, allowing for easy user manipulation (deleting/adding specific motifs, introducing IUPAC degeneracy symbols, etc).
  • ProcessFASTA — Process a sequence file in FASTA format to select a list of sequences based on their IDs, convert to reverse complement, combine ID and sequence into a single line, etc.
  • ProcessTdat — Manipulate tab-delimited measurement files (extract a subset of experiments, perform log-transformation, sort entries by ID, etc).
  • ExtractWindows — Extract subsequences from larger sequences (e.g., a chromosome), based on a set of start/end coordinates.
80
Documentation / Set up the REDUCE Suite
« Last post by xiangjun on April 21, 2016, 11:13:30 am »
Starting from REDUCE Suite v2.2, we've streamlined the downloading process. Users just need to register on this Forum, and log in to see the member-only download section (at the upper-left corner). The Suite is distributed with the source code (in ANSI C) available. Moreover, for user convenience, we have compiled the Suite on common operating systems, including Mac OS X, Linux (64-bit), and Windows (via Cygwin).

Assume you have at least basic knowledge of Linux (Unix/Mac OS X) and know how to use the shell, getting the REDUCE Suite up and running is a really simple process. It involves to set up an environment variable REDUCE_SUITE so the system knows where the Suite has been installed, and an update of your command PATH so that you can run the associated programs conveniently. The whole process is further facilitated by the REDUCE_Suite_setup script, as shown below:

Code: [Select]
To install the REDUCE Suite, do as follows:
  (0) Download the Suite from http://reducesuite.bussemakerlab.org/.
      You also need to have Perl installed for the setup step.
      Note that you *must* register and log in to see the download page.
      Assuming your downloaded tarball is for the macOS:
          REDUCE-Suite-v2.2-macosx-intel.tar.gz

  (1) tar zxvf REDUCE-Suite-v2.2-macosx-intel.tar.gz
        This will create a directory named REDUCE-Suite-v2.2/

  (2) cd REDUCE-Suite-v2.2/
        You are now in the REDUCE-Suite-v2.2/ directory

  (3) >>> [optional] ONLY IF you compile REDUCE Suite from source <<<
        (3a) cd src/
        (3b) make
        (3c) cd ../   # back to REDUCE-Suite-v2.2/, as with step (2)

  (4) ./bin/REDUCE_Suite_setup    # assuming you are at directory: REDUCE-Suite-v2.2/
        To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
          --------------------------------------------------------------
            export REDUCE_SUITE='/Users/xiangjun/Luxes/REDUCE_Suite'
            export PATH='/Users/xiangjun/Luxes/REDUCE_Suite/bin':$PATH
          --------------------------------------------------------------

         and then logout and login again, or run the following command:
              source ~/.bashrc

  (5) type MatrixREDUCE -h
           LogoGenerator -h
           HTMLSummary -h
      etc for command-line help and worked examples

  (6) Note: to use HTMLSummary for the summary page, you need to install
            GhostScript. See $REDUCE_SUITE/config/pkg_settings.cfg for
            setting path to the command 'gs'. LogoGenerator generates
            the logo image in EPS format, and uses 'gs' to convert EPS
            into PDF, PNG, or JPG. Additionally, with ImageMagick, you
            can also get the logo image in GIF.

The above instruction should help get you started with the Suite. If you have any questions, please do not hesitate to ask. The Forum has been created for any related questions, comments, or suggestions.

Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org