helix% gcg_paup myfile.script

 #NEXUS 

 begin trees;  [Treefile saved Fri May  8 10:41:54 1998]
 [!>Tree(s) input to PAUP* as user-defined tree(s)
 ]
         translate
                 1 chpdrbbq,
                 2 chpdrbbs,
 
                 3 chpdrbbd,
                 4 chpdrbca,
                 5 chpdrbae,
                 6 chpdrbag
                 ;
 tree PAUP_1 = ((1:0,2:1):26,((3:2,4:1):19,(5:7,6:6):12):0);
 end;

This file (called myfile.rooted by default) will work as input to TreeView.

Information courtesy of Eric Cabot, GCG inc.

I need to compare my 200 bp sequence against a complete virus genome, which is 124,000 bases long. How should I do this?

• One way is to run Fasta against the genome sequence. If the genome sequence is in Genbank, you can pull it out with the GCG 'fetch' command. Then run Fasta as follows:

  helix% fasta FastA does a Pearson and Lipman search for similarity between a query sequence and a group of sequences of the same type (nucleic acid or protein). For nucleotide searches, FastA may be more sensitive than BLAST. 11-Nov-1997 FASTA with what query sequence ? mysequence.gcg Begin (* 1 *) ? End (* 50 *) ? Search for query in what sequence(s) (* GenEMBL:* *) ? hevzvxx.gb_vi What word size (* 6 *) ? Don't show scores whose E() value exceeds: (* 2.0 *): What should I call the output file (* mysequence.fasta *) ? 1 Sequences 124,884 bp searched hevzvxx.gb_vi (Nucleotide) FASTA of: test.gcg from: 1 to: 50 June 22, 1998 10:39 TO: hevzvxx.gb_vi Sequences: 1 Symbols: 124,884 Word Size: 6 Searching with both strands of the query. Scoring matrix: GenRunData:fastadna.cmp Constant pamfactor used Gap creation penalty: 16 Gap extension penalty: 4 The best scores are: init1 initn opt hevzvxx.gb_vi ! LOCUS HEVZVXX 124884 bp ... 250 250 250 hevzvxx.gb_vi ! LOCUS HEVZVXX 124884 bp ... 55 80 56 The list contains 2 entries. How many alignments would you like to see (* 2 *) ? Aligning... CPU time used: Database scan: 0:00: 0.8 Post-scan processing: 0:00: 1.5 Total CPU time: 0:00: 3.0 Output File: mysequence.fasta

• As you can see, Fasta only found 2 entries -- basically, the best hit in the forward and backward direction. The genome is large, and so programs like Gap and Bestfit won't work, and anyway they will also give only the single best hit. An alternative approach would be to use the program Wordsearch followed by the program Segments. For example:

  helix% wordsearch WordSearch identifies sequences in the database that share large numbers of common words in the same register of comparison with your query sequence. The output of WordSearch can be displayed with Segments. WORDSEARCH with what query sequence ? mysequence.gcg Begin (* 1 *) ? End (* 1000 *) ? Search for query in what sequence(s) (* GenEMBL:* *) ? vi:hevzvxx What word size (* 6 *) ? List how many best diagonals (* 50 *) ? Integrate how many adjacent diagonals (* 3 *) ? What should I call the output file (* mysequence.word *) ? 1 HEVZVXX Len: 124,884 6-mers found: 1,045,257 Diagonals with words: 24,879 Total diagonals: 251,766 Sequences searched: 1 CPU time: 00.53 Output file: mysequence.word

  The output from WordSearch is then typically passaged through the program Segments to produce a ".pairs" file. Here is what some of the the results of this search look like:

  (BestFit) SEGMENTS from: myfile.word May 22, 1998 14:29 (Nucleotide) WORDSEARCH of: /usr/users/share/cabot/test/temp/myfile.seq check: 2347 from: 1 to: 1000 ASSEMBLE January 13, 1998 16:44 Symbols: 1 to: 1000 from: dmrt412g ck: 5977, 1 to: 1000 LOCUS DMRT412G 6897 bp DNA INV 13-NOV-1996 DEFINITION Drosophila retrotransposon 412 genome. ACCESSION X04132 X03733 . . . AvMatch: 3.84 AvMisMatch: -6.00 GapWeight: 50 LengthWeight: 3 .. Match display thresholds for the alignment(s): | = IDENTITY : = 3 . = 1 myfile.seq check: 2347 from: 1 to: 1000 /Reverse GB_VI:HEVZVXX check: 4734 from: 70843 to: 124884 X04370 Varicella-Zoster virus complete genome. 9/93 Gaps: 1 Quality: 209 Ratio: 2.944 Score: 50 Width: 7 Limits: +/-8 . . . . . 989 CTCCGTTTTACAATATTTCTTACAATTTTTCTTATCTATATATATTTTAT 940 |||||| || ||||| | || | | || | |||| || | 70854 CTCCGTGTT.TTATATTATATCCACGGTGTTGATTCAACCAATATGTTGT 70902 . . 939 ATTTACTTTATATTTATATATA 918 || | |||| | ||| |||| 70903 ATCTTCTTTTTTTTTTACTATA 70924 myfile.seq check: 2347 from: 1 to: 1000 GB_VI:HEVZVXX check: 4734 from: 26311 to: 124884 X04370 Varicella-Zoster virus complete genome. 9/93 Gaps: 0 Quality: 112 Ratio: 7.000 Score: 46 Width: 8 Limits: +/-9 . 648 AGATAATATTAAAAAT 663 | ||| ||||| |||| 26964 ACATATTATTATAAAT 26979

• If the query sequence is relatively short (under 240 residues) then an alternate solution would be to use the program FindPatterns. Please be aware of the fact that, unless the optional qualifier "MISmatch" is included on the command line used to run FindPatterns, that only exact matches will be found. E.g:

     findpatterns -mis=2
  

• Yet another approach is to use the program BreakUp to break HEVZVXX into overlapping segments which can then be searched with FastA. You must first use Fetch to copy the entire sequence to a file in the current working directory. Here is an example, showing how to break the sequence into a series of 5 kb segments that overlap by 500 bases.

  % fetch vi:hevzvxx Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. hevzvxx.gb_vi % breakup -seg=5000 -over=500 BreakUp reads a GCG-format sequence file containing more than 350,000 sequence characters and writes it as a set of separate, shorter, overlapping sequence files that can be analyzed by Wisconsin Package programs. BREAKUP of what file(s) ? hevzvxx.gb_vi hevzvxx_00.gb_vi length: 5500 bp hevzvxx_01.gb_vi length: 5500 bp hevzvxx_02.gb_vi length: 5500 bp hevzvxx_03.gb_vi length: 5500 bp hevzvxx_04.gb_vi length: 5500 bp hevzvxx_05.gb_vi length: 5500 bp hevzvxx_06.gb_vi length: 5500 bp hevzvxx_07.gb_vi length: 5500 bp hevzvxx_08.gb_vi length: 5500 bp hevzvxx_09.gb_vi length: 5500 bp hevzvxx_10.gb_vi length: 5500 bp hevzvxx_11.gb_vi length: 5500 bp hevzvxx_12.gb_vi length: 5500 bp hevzvxx_13.gb_vi length: 5500 bp hevzvxx_14.gb_vi length: 5500 bp hevzvxx_15.gb_vi length: 5500 bp hevzvxx_16.gb_vi length: 5500 bp hevzvxx_17.gb_vi length: 5500 bp hevzvxx_18.gb_vi length: 5500 bp hevzvxx_19.gb_vi length: 5500 bp hevzvxx_20.gb_vi length: 5500 bp hevzvxx_21.gb_vi length: 5500 bp hevzvxx_22.gb_vi length: 5500 bp hevzvxx_23.gb_vi length: 5500 bp hevzvxx_24.gb_vi length: 4884 bp

  You can then use an ambigous file specification such as "hevzvxx_*.gb_vi" with to perform a FastA to search against the the files produced by BreakUp. I recommend that you also include the optional qualifier NOSTATs the FastA command line in order to suppress the calculation of E() statistics. For example:

  % fasta -nostat FastA does a Pearson and Lipman search for similarity between a query sequence and a group of sequences of the same type (nucleic acid or protein). For nucleotide searches, FastA may be more sensitive than BLAST. FASTA with what query sequence ? mysequence.gcg Begin (* 1 *) ? End (* 1000 *) ? Search for query in what sequence(s) (* GenEMBL:* *) ? hevzvxx_*.gb_vi

How do I kill a paupsearch batch run?

For a batch run, however, the program is running on another computer, and it is not as easy to kill the program. During normal working hours, you can call up the helix staff (4-DCRT) and ask them to kill it for you. If you want to kill it yourself, you need to rlogin