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Spin is an interactive and graphical program for analysing and comparing sequences. It contains functions to search for restriction sites, consensus sequences/motifs and protein coding regions, can analyse the composition of the sequence and translate DNA to protein. It also contains functions for locating segments of similarity within and between sequences, and for finding global and local alignments between pairs of sequences. To help assess the statistical significance of comparisons the program can calculate tables of expected and observed score frequencies for each score level. Most analytical functions which operate on single sequences add their graphical results to a "SPIN Sequence Plot" that is associated with the sequence being analysed. (An exception is the restriction enzyme search which produces its own separate window.) Most functions which compare pairs of sequences add their results to a "SPIN Sequence Comparison Plot". The SPIN Sequence Plot and the SPIN Sequence Comparison Plot each have associated sequence display windows: the Sequence Display and the Sequence Comparison Display. These allow the text of the sequences to be viewed and use cursors to show the corresponding positions in the graphical displays. The graphical plots can be zoomed, and cursors or crosshairs can be used to locate the positions of the individual results. Plots can be superimposed.

Summary of the Spin Single Sequence Functions

Spin's main single sequence analytical functions are accessed via the Statistics, Translation and Search menus. The "Statistics" menu contains options to count and plot the base composition ( see section Plot base composition) and also to count the dinucleotide frequencies ( see section Count Dinucleotide Frequencies).

The "Translation" menu contains options to set the genetic code ( see section Set genetic code), translate to protein ( see section Translation - general), find open reading frames and write the results in either feature table format or as fasta format protein sequence files ( see section Find open reading frames), and to calculate codon tables.

The "Search" menu contains a variety of different searching techniques. "Protein genes" has four methods for finding protein genes ( see section Codon usage method) ( see section Author test), ( see section Positional base preferences) (accessed as a subcomponent of the Codon Usage Method), and ( see section Uneven positional base preferences). There is also a method to search for tRNA genes ( see section tRNA search). It is also possible to perform subsequence or string searches ( see section Subsequence search) and restriction enzyme searches ( see section Restriction enzyme search). There are searches for start ( see section Start codon search) and stop codons ( see section Stop codon search), splice junction searches ( see section Splice site search), and general motif searches using weight matrices ( see section Motif search).

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This page is maintained by staden-package. Last generated on 22 October 2002.