cladimo.bx.psu.edu

CladiMo

1) Alignment or sequence. Alignment in MAF format. MAF - - · Example. Middot; UCSC definition. Sequence in FASTA format. FASTA - - · Example. Middot; NCBI definition. Instructions for obtaining input from Galaxy. Middot; Genome Browser. Paste-in, upload sequence/alignment. Upload a local file. Paste raw text or a URL. List motifs, separated by spaces. e.g. WGATAR TATAA. A Motif must consist of IUPAC symbols. See table below. 3-fold and 4-fold degenerate symbols are not used. Paste-in, upload PWM.

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CladiMo | cladimo.bx.psu.edu Reviews

<META> DESCRIPTION

1) Alignment or sequence. Alignment in MAF format. MAF - - · Example. Middot; UCSC definition. Sequence in FASTA format. FASTA - - · Example. Middot; NCBI definition. Instructions for obtaining input from Galaxy. Middot; Genome Browser. Paste-in, upload sequence/alignment. Upload a local file. Paste raw text or a URL. List motifs, separated by spaces. e.g. WGATAR TATAA. A Motif must consist of IUPAC symbols. See table below. 3-fold and 4-fold degenerate symbols are not used. Paste-in, upload PWM.

<META> KEYWORDS

1 cladimo

2 2 motif

3 specify motif s

4 iupac symbols

5 nucleotide symbols

6 adenine a

7 cytosine c

8 guanine g

9 thymine t

10 2 fold degenerate symbols

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cladimo,2 motif,specify motif s,iupac symbols,nucleotide symbols,adenine a,cytosine c,guanine g,thymine t,2 fold degenerate symbols,and/or pwm,upload file,jaspar accession,3 output,view results,in this window

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CladiMo | cladimo.bx.psu.edu Reviews

https://cladimo.bx.psu.edu

1) Alignment or sequence. Alignment in MAF format. MAF - - · Example. Middot; UCSC definition. Sequence in FASTA format. FASTA - - · Example. Middot; NCBI definition. Instructions for obtaining input from Galaxy. Middot; Genome Browser. Paste-in, upload sequence/alignment. Upload a local file. Paste raw text or a URL. List motifs, separated by spaces. e.g. WGATAR TATAA. A Motif must consist of IUPAC symbols. See table below. 3-fold and 4-fold degenerate symbols are not used. Paste-in, upload PWM.

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Galaxy instructions

http://cladimo.bx.psu.edu/galaxy_instructions.xhtml

1) Define genomic intervals. Can be a file on your computer, or a URL to a file. You can also paste in data. An interval from an enhancer in the mouse genome (mm8). Add the data to your history page, to use as input to the tool that extracts the MAF alignment.

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wiki.bx.psu.edu

HLab:Main - CCGB

http://wiki.bx.psu.edu/HLab:Main

Hi, the is the wiki "HOME" for Hardison Lab. Everyone is welcome to edit it. This contains our laboratory protocols and other resources. If you are a visitor and interested in the lab projects, please go this way to the Hardison lab homepage. If you are a member of this lab, you can use your login name and password to access our database: HLab:HardisonData. Or view meeting notes. Search tool for conserved motifs. An interactive Flash tool for exploring MAF alignment files. Weekly Genomics Seminar schedule.

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CladiMo

1) Alignment or sequence. Alignment in MAF format. MAF - - · Example. Middot; UCSC definition. Sequence in FASTA format. FASTA - - · Example. Middot; NCBI definition. Instructions for obtaining input from Galaxy. Middot; Genome Browser. Paste-in, upload sequence/alignment. Upload a local file. Paste raw text or a URL. List motifs, separated by spaces. e.g. WGATAR TATAA. A Motif must consist of IUPAC symbols. See table below. 3-fold and 4-fold degenerate symbols are not used. Paste-in, upload PWM.

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