Given a set of DNA sequences that share a common function, ab initio cis-element search programs can be used to identify which motifs are the best conserved in the set. Specialties and references to these programs are:
Sequences may be entered in Fasta, raw, or GenBank format. Any non-alphabetic characters in the sequence will be ignored, and any alphabetic characters except A, C, G and T (uppercase or lowercase) will be converted to 'n' and excluded from matching motifs. If GenBank format is used, your program of choice will read and display any 'CDS' (protein-coding region) annotations. Limits: at most 50 sequences, of total length up to 100 kb.
For example GenBank accession numbers (e.g. NC_001669), 'accession.version' numbers (e.g. NC_001669.1), or GI numbers (e.g. 9628421).
Generic format ('|' means or, '' means optional) :
Enjoy this mess for now, examples coming soon :)
|-a||minimum alignment width (1)|
|-b||maximum alignment width (10000)|
|-c||cooling factor (1)|
|-d||frequency of width-adjusting moves (1)|
|-l||("ell") filter lowercase letters|
|-m||use modified Lam schedule (default = geometric schedule)|
|-n||end each run after this many iterations without improvement (10000)|
|-p||pseudocount weight (1.5)|
|-q||pretend residue abundances = 1/4|
|-r||number of alignment runs (10)|
|-s||seed for random number generator (1)|
|-t||initial temperature (0.9)|
|-u||use uniform pseudocounts: each pseudocount = p/4|
|-v||verbose: print suboptimal alignments|
|-z||turn off ZOOPS (force every sequence to participate in the alignment)|
|-1||("one") just examine forward strand (default = both strands)|
To save computing time, you can upload a file containing previously saved text output for visualization purposes, after you input the proper sequence information. Please assure the integrity of your input text file. You should either redirect command-line program output to a text file, or save text output at the end of MotifViz result page into a text file.
Please visit the following pages for directions on downloading currently-supported programs:
Internet Explorer 5.2+ is recommended for Mac users.
Form entries | Gene Regulation Hub | Suggestions to: Yutao Fu 07/27/06 14:00 EDT