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Nucleic Acids Res 10: 279-94 (1982)[82150184]

SEQ: a nucleotide sequence analysis and recombination system.

D. L. Brutlag, J. Clayton, P. Friedland & L. H. Kedes

SEQ is an interactive, self-documenting computer program that contains procedures for the analysis of nucleotide sequences and the manipulation of such sequences to allow the simulation and prediction of the results of recombinant DNA experiments.

The SEQ analysis system provides an interactive environment for the analysis of data obtained from nucleotide sequencing and for the simulation of recombinant DNA experiments. The interactive environment and the self.documenting nature of the program make it easy for the non-programmer to use. SEQ prompts the user for each piece of information required and the response is most often a single number or a letter. The program is particularly helpful for the inexperienced user in that typing a question mark at any point will provide for the user a description or what the program expects. SEQ's responses to question marks form a short tutorial on the program itself. In addition, all errors made by the user are explained in plain English so that appropriate responses can be made.

While the various procedures of the SEQ program are related to many other programs of similar purpose , SEQ has a rapid and improved homology and dyad symmetry search algorithm which finds many homologies and dyad symmetries that are overlooked-by earlier algorithms. SEQ also prepares restriction maps with the names and locations of the restriction sites marked on the nucleotide sequence as well as tables containing the length of DNA fragments produced by restriction digests of any known sequence. SEQ treats circular sequences properly for all of its search and comparision functions.

SEQ contains 13 primary procedures with over 25 additional suboptions that allow sequence data to be displayed and analyzed in a wide variety of ways. The user can analyze any sequence, any part of a sequence, the inverse-complement of a sequence, or any combination of parts of sequences. In addition, any new sequences generated by the combination of parts of sequences can be saved and can serve as a permanent record for later analysis. It is this capability to combine parts of sequences

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