Using List Files

A list file, formerly known as a file of sequence names, is what its name implies: a file containing a list of sequence names and their locations. You can think of list files as a way to organize your sequences on a project-by-project basis.

You will find list files useful for specifying sequences from multiple files in one file that you can use as input to a program. List files can contain any number of the following types of sequences:

• Single sequences from the databases or your personal directories, for example, GB_In:Dro5S or /smith/project/gamma.seq.

  　

• Database sequence names using asterisk (*) wildcards, for example GenBank:Hum*. Note that you cannot use wildcards to include multiple sequence files from your personal directories, for example /smith/project/*.seq.

  　

• Names of other list files, for example, @hsp70.list.

  　

• Sequences in RSF or MSF files, for example
  pileup.msf{ssa4} or hsp.rsf{*}.

  　

You can use list files with any program that accepts multiple sequences as input. A program prompt asking "What sequence(s)?" implies that the program accepts multiple sequences.

Below is an example of a list file.

Figure 4

In addition to sequence specifications, each sequence in a list file may optionally contain sequence attributes. These attributes include:

Begin Position. (Begin:n) Shows the base position you want to start with, where n= 1 to the length of the sequence.

End Position. (End:n) Shows the base position you want to end with, where n = 1 to the length of the sequence.

Strand. (Strand:+ or -) Defines the forward or reverse complement nucleic acid sequence strand, where + = forward strand and - = reverse strand.

Sequence Topology: Linear or Circular. (Circ:T or F) Defines the strand as linear or circular, where T = circular and F = linear.

Sequence Weight. (Wgt:n.n) Defines the sequence weight, or the significance of the sequence in comparison to other sequences. That is, you may not want all sequences accounted for equally to determine a result. Therefore, you can give some sequences greater weight than others. This attribute is of use only when you are using two or more sequences in the analysis.

Join. (Join:Sequence_Name) Indicates that the sequence segment should be concatenated with the next sequence in the list that has an identical Join: Sequence_Name attribute. Several contiguous sequences specified in a list file with the same Join:Sequence_Name attribute are concatenated together. (Assemble, Translate, and LookUp are the only Wisconsin Package programs that use the Join attribute. SeqLab uses the Join attribute to concatenate list file sequences in the Editor.)

Note: In Version 9.0 or later, the following programs use some or all of these sequence attributes in the command-line version of the Package: Assemble, CodonFrequency, Distances, Diverge, FrameSearch, PileUp, PlotSimilarity, ProfileMake, Seg, Translate, and Xnu.

Creating and Editing List Files by Hand

To create a list file with a text editor:

1. Open a new file with the text editor of your choice, for example vi.

   　

2. Type the appropriate information. A list file contains the following optional and required elements (see the list file example earlier in this section):

   　

   File Type. (optional) Begins with the line (all uppercase) !!SEQUENCE_LIST 1.0. SeqLab uses the file type to improve performance when loading files. Do not edit or delete the file type. If present, it must appear on the first line of the file.

   Description. (optional) Contains informative text, including the date of creation, describing what is in the file.

   Dividing Line. (required) Includes two periods (..) that must appear on the line preceding the sequence list.

   Sequence List. (required) Includes the single sequences from your personal directory or a database, sequence specifications using wildcards, RSF files, MSF files, or list files. You must provide the database or directory specification. You can add sequences in any order.

   Sequence Attributes. (optional) Can include the begin and end position, indicate the forward or reverse strand, define the strand as linear or circular, give the sequence a weight in comparison with other sequences, and indicate whether the sequence is concatenated with other sequences in the list.

   Sequence Comments. (optional) Includes an exclamation point (!) followed by a short comment or definition of the sequence(s) or list file.

3. Save and exit the file.

   　

To edit a list file, either one you have manually created or one created by a program:

Use a text editor of your choice and modify the file as necessary.

TIP - One way to specify a subset of sequences is to "comment out" those unwanted sequences within the list file. If you comment out sequences instead of deleting them, you can use them at a later time.

To comment out sequences:

1. Open the list file in the text editor of your choice and find the sequences you do not want to use.

   　

2. Type an exclamation point (!) in front of the name of each sequence you do not want. For example
   

   Figure 5

   　

   　

3. Save the file and exit the text editor.

   　

4. To specify the list file, type an at sign (@) followed by the list filename and extension, for example @hsp70.list. The program will use only those sequences that are not commented out.
   

   　

Programs That Create List Files

Some Wisconsin Package programs can produce output in list file format. Any program that creates multiple sequence output files and can organize those sequence specifications in a list file supports the -LIStfile parameter. You can then use that list file as input to other programs.

Programs that can create list output files and their parameters (if necessary) are listed below.

Note: Some of the programs listed above, such as LineUp and ProfileSearch, may include additional program-specific information in the output list file. Others, such as FastA and BLAST, may include sequence alignments. This extra information does not affect the list file's performance.

Specifying List Files

To specify a list file in response to a program prompt:

Type an at sign (@) and the name of the list file and extension, for example @hsp70.list.

Note: You cannot use wildcards to specify a list file. For example, you cannot specify @hsp*.list.