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51
Documentation / MotifREDUCE
« Last post by xiangjun on September 27, 2016, 02:39:42 pm »
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, REDUCE makes it possible to find regulatory elements based on a single microarray experiment. MotifREDUCE in the REDUCE Suite is a more robust and efficient reimplementation of the "original REDUCE algorithm" by Bussemaker et al (2001).

MotifREDUCE [options] -sequence=seqfile -measurement=measfile

  Required parameters:
    -sequence=seqfile     --- sequence file in FASTA format
    -meas=measfile        --- measurement (expression/binding) file in tab-delimited format

  Optional parameters:
    [-topo_list=topofile]  --- name of topology file (up_to_octamers)
    [-topo=topology]       --- single topology pattern, e.g., X3--X4
    [-dicfile=file]        --- list of motifs to check against. IUPAC wild cards
                                   allowed; no length limit
    [-ntop=integer]        --- number of top seed motifs to print out (10)
    [-iupac_pos=integer]   --- number of positions to check for IUPAC degeneracy (0)
    [-iupac_sym=string]    --- IUPAC symbols to check against ('KMRSWYBDHVN')

    [-output=dir_name]     --- path to the output directory (./)
    [-p_value=float]       --- threshold to stop looking for new motifs (0.001)
    [-max_motif=integer]   --- maximum # of motifs to search (20)
    [-strand=integer]      ---  1 |+1 |F | L for leading strand;
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                0 | A |D     auto-detection (check 1 and 2)

    [-runlog=[stderr|stdout|file]]
                           --- direct running diagnostics message to stderr,
                                   stdout or a specific file (stderr)
    [-help]                --- print out this help message

  Usage:
    mkdir -p results   # use topology file (up_to_heptamers)
    MotifREDUCE \
        -meas=$REDUCE_SUITE/examples/MotifREDUCE/yeast_sample.csv \
        -sequence=$REDUCE_SUITE/examples/MotifREDUCE/genome5pns600.fasta \
        -topo_list=$REDUCE_SUITE/examples/MotifREDUCE/up_to_heptamers \
        -o=results
    HTMLSummary -c -o=results

Notes:
  • The command-line user-interface of MotifREDUCE is identical to that of MatrixREDUCE, but skips the Levenberg-Marquardt non-linear least-squares optimization of weight matrix (Ws). The result is a list of motifs, which are expressed in matrix form with 1s and 0s.
  • The above example dataset takes ~10s and finds 10 significant motifs on a contemporary laptop computer.
52
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 27, 2016, 02:01:22 am »
Hi Xiang-Jun,

Got it! And thanks a lot for the information about logo colors :D

Best,
Kate
53
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
54
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
55
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
56
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.
57
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
58
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

59
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
60
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 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).

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
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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