Using Rich Sequence Format (RSF) Files

A Rich Sequence Format (RSF) file contains one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be richly annotated with descriptive sequence information such as:

• Creator/author of the sequence

  　

• Sequence weight

  　

• Creation date

  　

• One-line description of the sequence

  　

• Offset, or the number of leading gaps in a sequence that is part of an alignment or fragment assembly project

  　

• Known sequence features

  　

RSF files are powerful for using with SeqLab, the graphical user interface to the Wisconsin Package. Because they store positional information, you can display RSF files within SeqLab's Editor mode to view and edit sequence alignments and features. The features annotation allows you to graphically view and align sequences based on features as well as run programs on sequence regions selected by feature. You also will find RSF files useful for distributing sequences to colleagues, since these files contain each sequence's data and descriptive information.

Note: If you plan on using SeqLab for the bulk of your analyses, it is best to save your files as RSF if possible. RSF files are more richly annotated than list files or MSF files, which do not save sequence features information as part of the file.

Below is an example of an RSF file.

Figure 6

You may find the following components in an RSF file:

• File Type. (required) Begins with the line (all uppercase) !!RICH_SEQUENCE 1.0. SeqLab uses the file type to improve performance when loading files. Do not edit or delete the file type. It must appear on the first line of the file.

  　

• Dividing Line. (required) Includes two periods (..) that must appear on the line preceding all sequence information and data. Optional comments may appear between the file type and dividing line.

  　

• Sequence Attributes. Includes descriptive information about the sequence, such as name, sequence description, sequence type, creator, offset, creation-date, strand, weight, and comments. If the sequence is from a database, this section also includes any taxonomic and bibliographic information about the sequence, compiled by the original database.

  　

• Features. (optional) Contains the features information, including sequence range, description, and graphical depiction. Consider the following example of features information from an RSF file:

  Figure 7

  　

  　

  The colors, shapes, and fill patterns depicted in SeqLab's Editor are defined in a resource file called feature.cols. To customize these attributes, copy feature.cols to your current directory by typing % fetch feature.cols. Then edit the file in the text editor of your choice, for example vi. The file is internally documented.

• Sequence. (required) Contains the sequence data.

  　

Programs That Create RSF Files

To create an RSF file:

Choose from the following.

• SeqLab. You can save files in RSF format from within SeqLab's Editor. For more information, see "Saving Your Work" in Chapter 2, Editing Sequences and Alignments in the SeqLab Guide.

  　

• Wisconsin Package programs. The Wisconsin Package programs and their parameters (if necessary) that create RSF files are listed below.

  Program	Parameter (if necessary)
  CoilScan	-RSF
  FindPatterns	-RSF
  FrameSearch	-RSF
  HTHScan	-RSF
  Map	-RSF
  Motifs	-RSF
  MotifSearch	-RSF
  NetFetch
  PeptideMap	-RSF
  PeptideStructure	-RSF
  Prime	-RSF
  Reformat	-RSF
  SPScan	-RSF

Editing RSF Files

To edit an RSF file:

Use SeqLab. If you load an RSF file into SeqLab's Editor, it graphically displays the sequences in the file. For more information, see Chapter 2, Editing Sequences and Alignments in the SeqLab Guide.

You can also use a text editor to modify an RSF file. If you do, however, the file's checksum changes, and Wisconsin Package programs will not recognize the file. Therefore, if you use a text editor to modify an RSF file, you must use the Reformat program with the -RSF parameter to rewrite the file into GCG format.

Specifying RSF Files

To specify a single sequence, a subset of sequences, or all sequences within an RSF file:

Choose one of the following.

• Single Sequence. To specify a single sequence within an RSF file, type the name of the RSF file and extension followed by the name of a sequence in curly brackets, for example opsin.rsf{opsf_human}.

  　

• Multiple Sequences. To specify a subset of sequences or all sequences within an RSF file, type the name of the RSF file and extension followed by a file specification and/or asterisk (*) wildcard in curly brackets. For example, opsin.rsf{opsg*} specifies all sequences in opsin.rsf beginning with "opsg"; opsin.rsf{*human*} specifies all sequences in opsin.rsf where "human" is part of the sequence name; and opsin.rsf{*} specifies every sequence in opsin.rsf.