Here is a sample session with showseq % showseq tembl:paamir -sbeg 1 -send 100 Display a sequence with features, translation etc.. Things to display 0 : Enter your own list of things to display 1 : Sequence only 2 : Default sequence with features 3 : Pretty sequence 4 : One frame translation 5 : Three frame translations 6 : Six frame translations 7 : Restriction enzyme map 8 : Baroque Display format [2]: Output file [paamir.showseq]: Go to the input files for this exampleGo to the output files for this example Example 2 The standard list of output formats are only a small selection of the possible ways in which a sequence might be displayed. Precise control over the output format is acheived by selecting the qualifier '-format 0' (Option 0 in the list of things to display). For example, by choosing format '0' and then specifying that we want to display the things: 'b,s,t,c', we will output the sequence in the following way: % showseq tembl:paamir -sbeg 1 -send 120 Display a sequence with features, translation etc.. Things to display 0 : Enter your own list of things to display 1 : Sequence only 2 : Default sequence with features 3 : Pretty sequence 4 : One frame translation 5 : Three frame translations 6 : Six frame translations 7 : Restriction enzyme map 8 : Baroque Display format [2]: 0 Specify your own things to display S : Sequence B : Blank line 1 : Frame1 translation 2 : Frame2 translation 3 : Frame3 translation -1 : CompFrame1 translation -2 : CompFrame2 translation -3 : CompFrame3 translation T : Ticks line N : Number ticks line C : Complement sequence F : Features R : Restriction enzyme cut sites in forward sense -R : Restriction enzyme cut sites in reverse sense A : Annotation Enter a list of things to display [B,N,T,S,A,F]: b,s,t,c Output file [paamir.showseq]: Go to the output files for this example Example 3 Display only the sequence: % showseq tembl:paamir -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example Example 4 Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'): % showseq tsw:rs24_fugru -three -format 2 Display a sequence with features, translation etc.. Output file [rs24_fugru.showseq]: Go to the input files for this exampleGo to the output files for this example Example 5 Number the sequence lines in the margin: % showseq tembl:paamir -sbeg 1 -send 100 -format 1 -number Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example Example 6 Start the numbering at a specified value ('123' in this case): % showseq tembl:paamir -sbeg 1 -send 100 -format 1 -number -offset 123 Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example Example 7 Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase). % showseq tembl:paamir -sbeg 1 -send 100 -format 1 -slower -upper '25-45,101-203,333-362' Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example Example 8 Translate selected regions: % showseq tembl:paamir -sbeg 1 -send 120 -format 4 -trans 25-49,66-76 Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example Example 9 Add your own annotation to the display: % showseq tembl:paamir -sbeg 1 -send 100 -format 2 -send 120 -annotation '13-26 binding site 15-15 SNP' Display a sequence with features, translation etc.. Output file [paamir.showseq]: Go to the output files for this example
