Search genome TMHMM results for given text



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


	

	

		

			

	

		

			
				

					

						Choose genome database :
						
							
						
					

				

					
		

		

			
				

					

						
							

								

									
										

											

												Enter search text : 
												
													

														

															
																
																

																	
														

													

														
											

											

												
													


													
													     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 :


										amino acid sequence (of Entrez Protein genes)
										FASTA identifier
										these exact charges
										show all genes (ignore the "Enter search text" box)
										
          ...and...

										TMHMM results show number of TMS (transmembrane segments) is :
										          from  to 
										          For this search type, enter 2 whole number integers.

										          eg. from 2 to 6

										          eg. from 9 to 9

										          eg. from 1 to 1000

										
          ...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
										

										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
										
For each sequence, display the graphics results from :

										

							

								
					

				

					
		

	


					
		

	


	

	


	

		
		
	

	

	

		

			
		

	

	



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/searchtmhmm.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