Search genome ORF interproscan results for given text

searchgenome.cgi
searchorf.cgi
searchtmhmm.cgi
convertcharges.cgi

	

	

		

			


	

		

			

				

					

						
Choose ORF database :
						

							
								Streptococcus pneumoniae D39, all ORFs (of length 40 or more) (59704 seqs)
								Streptococcus pneumoniae D39, all ORFs (of length 60 or more) (18081 seqs)
								Streptococcus pneumoniae D39, all ORFs (of length 40 to 59) (41623 seqs)
								Streptococcus pneumoniae D39, all ORFs (of length 50 to 59) (13400 seqs)
								Streptococcus pneumoniae D39, all ORFs (of length 40 to 49) (28223 seqs)
								Streptococcus pneumoniae D39, TVGYG-like ORFs, identified manually (54 seqs)
								Streptococcus pneumoniae D39, TVGYG-like ORFs, identified manually from Trk (20 seqs)
								Streptococcus pneumoniae D39, TVGYG-like ORFs, identified by EMBOSS emma (77 seqs)
							
						
					
				
			
		
		

			

				

					

						

							

								

									

										

											

												
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.

																eg.

																

																	
sodium-calcium
Na+
NaCa
																	
sodium calcium
Ca+
PF00004
																	
sodium/calcium
K+
TIGR01241
																
															
														
													
												
											
											

												

													


													
													     or     
													
													



												
											
											

												
Enter pattern pieces : 
												

													

														

															

																
																

																Enter pattern pieces, separated by commas. eg.

																.-..++.,.+.+.,.+..-.

																               will match :

																....-..++..-.-...+-+....+.+.....+..-......

																               and will be displayed as :

																___1111111_____________22222___333333_____

																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 :

																     20,MIGW,CVLAL,LLK,0,PTTV,CLASA


																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.

																eg.

																-------MMIETLR------AIGLVVFMQLLSLALEF---

																--------MIETLK------AIGLVVFMQLLSLALEF---

																-----MWMNFESLQIAR-AYLFGEVKYLDLMLVLNII--D

																or

																       ...-..+      ...............-.   

																        ..-..+      ...............-.   

																     .....-.....+ .....-.+..-........  -

																

																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)
										
          ...and...

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

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

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

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

										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
										
										--don't search or display homemade HMMERs--
											K-channels TVGYG-like
											TVGYG-filter
											K-channels non-TVGYG-half
											K-channels non-TVGYG-half spacey-align
											Wang 2000 all holins
											Wang 2000 class 1 holins
											Wang 2000 class 2 holins
											Wang 2000 gram +ve class 1 holins
											Wang 2000 gram -ve class 1 holins
											Wang 2000 gram +ve class 2 holins
											Wang 2000 gram -ve class 2 holins
											Wang 2000 class other holins
											Wang 2000 gram +ve class other holins
											Wang 2000 gram -ve class other holins
											Wang 2000 unconventional holins
											DUMMY CHRGS Wang 2000 class 1 holins
											DUMMY CHRGS Wang 2000 class 2 holins
											DUMMY CHRGS Wang 2000 gram +ve class 1 holins
											DUMMY CHRGS Wang 2000 gram -ve class 1 holins
											DUMMY CHRGS Wang 2000 gram +ve class 2 holins
											DUMMY CHRGS Wang 2000 gram -ve class 2 holins
											Wood 1995 K-chan pores
											Wood 1995 glut-receptor pores
											Wood 1995 K-chan/glut-receptor pores
											Wood 1995 K-chan/glut-recept/other pores
											Wood 1995 other pores
											Wo 1995 shaker pores
										

										when HMMER result exists for a sequence,
HMMER-matching domain displayed as :

										______XXXXXXXX______

										      evalue,score

										and having HMMER e-value  or lower
										and HMMER covers  % or more of the sequence
										
          ...and...

										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
										
          ...or...

										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
										
											Interproscan, then TMHMM
											TMHMM, then Interproscan
											only Interproscan
											only TMHMM
											neither Interproscan nor TMHMM
									
								
							
						
					
				
			
		
	

			
		
	

	
	


	

		
			K-channels TVGYG-like
			TVGYG-filter
			K-channels non-TVGYG-half
			K-channels non-TVGYG-half spacey-align
			Wang 2000 all holins
			Wang 2000 class 1 holins
			Wang 2000 class 2 holins
			Wang 2000 gram +ve class 1 holins
			Wang 2000 gram -ve class 1 holins
			Wang 2000 gram +ve class 2 holins
			Wang 2000 gram -ve class 2 holins
			Wang 2000 class other holins
			Wang 2000 gram +ve class other holins
			Wang 2000 gram -ve class other holins
			Wang 2000 unconventional holins
			DUMMY CHRGS Wang 2000 class 1 holins
			DUMMY CHRGS Wang 2000 class 2 holins
			DUMMY CHRGS Wang 2000 gram +ve class 1 holins
			DUMMY CHRGS Wang 2000 gram -ve class 1 holins
			DUMMY CHRGS Wang 2000 gram +ve class 2 holins
			DUMMY CHRGS Wang 2000 gram -ve class 2 holins
			Wood 1995 K-chan pores
			Wood 1995 glut-receptor pores
			Wood 1995 K-chan/glut-receptor pores
			Wood 1995 K-chan/glut-recept/other pores
			Wood 1995 other pores
			Wo 1995 shaker pores
		
		
	
	

	
	


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 www.canoz.com/ah/perl_programs_jan2009