By Annette M. Griffin, Hugh G. Griffin

Institute of foodstuff study, Norwich, U.K. equipment in Molecular Biology sequence, quantity 25. moment quantity finishing a pragmatic reduction for nucleic acid series researchers who use pcs to procure, shop, or learn their facts. Plastic comb binding. 15 members, five U.S.

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Additional info for Computer Analysis of Sequence Data Part II (Methods in Molecular Biology)

Sample text

The individual sequence readings derived from autoradiographs or from sequencing machines are initially stored in separate files, but the program copies them into the database during the assembly process. For normal operation, the program handles batches of readings-for example, 24 from a film or machine run. Batch processing is achieved by use of files of file names. Depending on the strategy employed and the stage of the project, the following operations may be performed. 1. Start a project database.

7. Joining Contigs Interactively Using XDAP The operation of the jom editor in XDAP is very similar to the one for single contigs described above. It allows the user to align the ends of the two contigs by editing each contig separately. First, specify which two contigs are to be joined. The program checks that the two contig numbers are different. ) The Join Editor consists of two Contig Editors m between which is sandwiched a disagreement box. This disagreement box uses exclamation marks to denote mismatches between the two consensuses.

2. ” The input file of file names. 3. ” This is a file of file names for those readings that do not contam the recognition sequences. Hence, it can be used for further processing of the batch. 4. Define “File name of recognition sequences,” which is the name of the file of recognition sequences. 3. Screening Against Vector Sequences For most strategies, it is necessary to compare readings against any vector sequences that may have been picked up during cloning. The package contains two routines for screening against vectors.

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