The current status and portability of our sequence handling software

@article{Staden1986TheCS,
  title={The current status and portability of our sequence handling software},
  author={Rodger Staden},
  journal={Nucleic acids research},
  year={1986},
  volume={14 1},
  pages={
          217-31
        }
}
  • R. Staden
  • Published 10 January 1986
  • Computer Science
  • Nucleic acids research
I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help… 
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References

SHOWING 1-6 OF 6 REFERENCES
Atlas of protein sequence and structure
Acorn BBC model B micro computer. Acorn, Cambridge
  • UK. (19) Deininger,P Anal. Biochem
  • 1969
Add Res. Acid Res. Nucl. Acid Res. Nucleic Acids Research
  • Add Res. Acid Res. Nucl. Acid Res. Nucleic Acids Research
  • 1977
The UNIX machine is called a Torch Unicorn and is made by Torch computers
  • The code for this 68000 based machine will be compatible with many others running under UNIX. (27) The terminal 1s called a VT640 and the modification for the VT100 is made by Digital Engineering Inc
  • 1981
28) Digital Equipment Corp
  • 28) Digital Equipment Corp
The UNIX machine is cal led a Torch Unicorn and is made by Torch computers, Aberley House, Shel ford, Cambridge, U.K. The code for t h i s 68000
  • Nature 298,
  • 1982