Sfixem---graphical sequence feature display in Java
TL;DR: UNLABELLED Sfixem is an sequence feature series (SFS) visualization tool implemented in Java designed to visualize data from sequence analysis programs, allowing the user to view multiple sets of computationally generated analysis to assist the analysis process.
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Abstract: Summary: Sfixem is an sequence feature series (SFS) visualization tool implemented in Java. It is designed to visualize data from sequence analysis programs, allowing the user to view multiple sets of computationally generated analysis to assist the analysis process. SFS is used as the data exchange format.
Availability: Sfixem is available for direct usage or download for local usage at http://sfixem.cgb.ki.se. A protein sequence analysis workbench using Sfixem is available at http://sfinx.cgb.ki.se.
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References
Artemis: sequence visualization and annotation.
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A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
TL;DR: DOTTER2, a dot-plot program for X-windows which can compare DNA or protein sequences, and also DNA versus protein, is presented here, and how DOTTER can improve gene modelling is illustrated.
825
ACeDB and macace.
Frank H. Eeckman,Richard Durbin +1 more
TL;DR: This chapter provides an overview of ACeDB for the C. elegans user, focusing in particular on the Macintosh version Macace, and describes methods to obtain ACe DB and documentation for it, ways to access and use the information inACeDB, and examines the use of ACEDB as a laboratory-based data managing system.
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GAIA: framework annotation of genomic sequence.
L. Charles Bailey,Stephen Fischer,Jonathan Schug,Jonathan Crabtree,Mark Gibson,G. Christian Overton +5 more
TL;DR: Results are presented for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and ways in which the current prototype can be improved.