Search genome ORF interproscan results for given text

Choose ORF database :
Enter search text :

Enter the exact texts to search for, one line per text.
The search is case insensitive. Capitals and lower case letters match each other.
Genes having at least one of these exact texts will be displayed.
sodium calciumCa+PF00004


Enter pattern pieces :

Enter pattern pieces, separated by commas. eg.
               will match :
               and will be displayed as :

To match a pattern pieces line, a sequence must match each pattern piece (separated by commas) in the presented order.
Sequences that match one or more pattern pieces lines will be returned.
Another example: To limit MIGW,CVLAL,LLK to span no more than 20 residues, whilst PTTV,CLASA has no length constraint, type in :

What type of pattern pieces have you entered?
amino acid residues (eg. TVGYG,PRSL,RIVGGV)
amino acid charges (eg. ..+-.-,..-+.-)
residues and charges (eg. TVGYG-IVP...,+.GGV)

Return sequences that match :
          from to pattern pieces lines above

Enter aligned charges or sequences :

Enter a multiple sequence alignment of charges or amino acid residues, one line per sequence.
       ...-..+      ...............-.   
        ..-..+      ...............-.   
     .....-.....+ .....-.+..-........  -

This alignment will be used to search for sequences in the database
that match every position in this template,
matching any character in the template at each template position.
If a sequence matches this multiple sequence alignment,
the matching area will be displayed as : ______MMMM______

What type of alignment have you entered?
amino acid residues (gaps denoted by '-')
amino acid charges (gaps denoted by spaces)
Choose search type :

Interproscan results text
amino acid sequence of ORF
FASTA identifier
these exact charges
show all ORFs (ignore the "Enter search text" box)


show all ORFs having Interproscan results
show ORFs having no informative Interproscan results
show all ORFs


TMHMM results show number of TMS (transmembrane segments) is :
          from to


all TMHMM results regardless of signal sequence
TMHMM results show possible signal sequence
TMHMM results do not show possible signal sequence


Only show sequences having the following amino acid lengths :
          from to


display results from the following homemade HMMER
only show sequences matching following HMMER
only show seqs with TMS matching following HMMER
only show seqs with non-TMS region matching HMMER

when HMMER result exists for a sequence,
HMMER-matching domain displayed as :
and having HMMER e-value or lower
and HMMER covers % or more of the sequence


Limit the number of sequences shown :
          from result number to result number

Choose display format :

display only amino acid sequences, not other results
display only charges, not even sequences or results
display only the database's sequence-id for the sequence
display only the database's fasta-id for the sequence


display all results, not just sequences or charges
Display polarity of amino acid residues
Display charges of amino acid residues
Display TMHMM results under amino acid residues

Note: If a query times out, then it is possible to run it from the command line in the following way. You will need a Perl environment to do so. Enter the query parameters as usual but don't press the "GO" button. Instead, press the "Create input for batch program" button. Perl parameter code will be displayed in your browser. Copy and paste it to a text file (eg. my_input.txt). On your computer, run the Perl program from the command line, indicating where the program, input file, and database files are found on your computer :      perl -T /usr/lib/cgi-bin/searchorf.cgi -infile my_input.txt -dbpath '/usr/lib/cgi-bin/' > my_output.html When it has finished running, double-click the output file (eg. my_output.txt) to view the output in a browser. The program and databases (and little images files called *.gif) can be found at