Introduction      Start      My Result      ReadMe

 Step-wise instruction

Step-wise instruction

l    Construction of model

 1 Input sequences in FASTA format/pre-aligned MSF

Multiple alignment via clustalW

Construct model by Hmmer2.0 package


The threshold in step 3 can be adjusted by user. The default setting is derived from the lowest score of hmmsearch with input sequences. There are three databases (Human, Mouse and Rat) can be used for hmmsearch. A notice will be sent to by email, after the whole process is finished. User can access the results using this account number (
2fldmg8m2f in example).

l    Data retrieval

Users retrieve result by account number in “My Result “session


Data access

     Sections of Result Access
a access the raw data and classification


View all:
the raw output from HMMER, which could be used in other cross ref.


GO clustering:
By GO, user annotates TF-regulated targets and has an insight in biological function of predicted transcriptome.
     l  Select one/more categories (molecular function/biological process/cellular
          component) for further analysis
     l  Examples of gene clustering by level 3 biological process

User could click blue box for detail information of the grouped genes
b Field searching: Retrieving results by  
    i Gene name/descriptions ex: FGF, growth fact  
    ii Gene Ontology term/Key words ex: growth, metabolism


  ENSG searching: Retrieving subset of results
      by known ENSG ID (list) ex: ENSG00000129991

d AFFY ID searching: Retrieving subset of results
      by known AFFYMETRIX microarray ID (list) ex: 205742_at

Typical output

ENSG ID: the gene ID in ensemble database


Gene description: full name of gene

ENST: the transcript IDs of the corresponding promoter sequence

Score: the bit score of found TF site in the promoter

Hit seq: the sequence of found TF site

Position: the position of found TF site related to transcription start site (TSS)

Orientation: the orientation of found TF site related to TSS.

GO characterization: the Gene Ontology classification of this gene in three categories.

InterPro characterization: the protein domain/family of the gene in interpro DB.




© By NCKU Bioinformatics Center , R.O.C. Government 2004. All Rights Reserved.