Sequencing in an X windows environment - A course.

D.P. Judge at VTVM2.CC.VT.EDU
Tue Aug 20 12:18:15 EST 1991

                              30/9/91 to 1/10/91

                         Trevor Hawkins & Rodger Staden

This two day course will give an practical introduction to the program XDAP
(Dear S and Staden R Nucleic Acids Research 19 3907-3911 (1991)).
XDAP is a new version of Rodger Staden's Sequence Assembly Program
(SAP) much enhanced to make full use of features available in an X windows

The course will use data from ABI 373A and Pharmacia A.L.F. fluorescent
sequencing machines, but it should be stressed that XDAP also handles
conventionally derived data and hence replaces SAP for those working in an
X windows environment.

The course will be run at the HGMP Resource Centre in Harrow. It is free to
all registered HGMP users. If you are a UK researcher in an appropriate field,
it is very likely that you are eligible to be a registered HGMP user
(registration is free). There should be plenty of time to register as an HGMP
user before the start of this course. For people who are not HGMP registered
users, course fees of 200 pounds per day will apply.

HGMP registered users have free access to a wide range of computing facilities
(including training courses). Facilities include a comprehensive range of
software and sequence and information databases. A number of the facilities
provided are not generally available elsewhere, including the GDB and OMIM
databases and login access to machines outside JANET (particularly useful
for obtaining public domain software and data from the USA). To register as an
HGMP user and/or to book a place on this course, please contact:

             Mrs Christine Bates,
             HGMP Resource Centre,
             Clinical Research Centre,
             Watford Road,
             MIDDX HA1 3UJ.

             Tel:  081 869 3446
             FAX:  081 869 3807

There follows the provisional timetable for the two days of the course. Please
note that the second afternoon has been largely set aside to deal with topics
suggested by course participants. It would be useful if you would indicate what
you would like to covered in this period when you book your place on the

At the time of writing, seven places are available on the 30/9/91 to 1/10/91
course. Further dates will be arranged as required.

                       PROVISIONAL COURSE TIMETABLE.

Monday 30/9/91:

 09:30 - 11:00    An introduction to the ABI and ALF automatic sequencing

                  Transferring sequence data from the automatic sequencer to
                  the system upon which the data will be analysed.

 11:00 - 13:00    Splitting the multi-sequence data files generated by the
                  automatic sequencers into single sequence data files.

                  "Clipping" the sequences. This involves, inspecting the trace
                  data produced by the automatic sequencer and the derived
                  sequences simultaneously. Regions at either end of each
                  sequence, where the reliability of the raw data is poor, are
                  marked and disregarded when overlaps between sequences are

 13:00 - 14:00    LUNCH

 14:00 - 17:30    Creation of a new sequencing project database.

                  Automatic entry of new sequence data into a sequencing
                  project database to form overlapping sets of sequences

                  Inspection of the contigs.

Tuesday 1/10/91:

 09:30 - 13:00    Editing a sequencing project database, including:

                    - Editing the contigs to correct the CONSENSUS sequence
                      (raw automatic sequencer data can be veiwed during
                      this process as well as the sequences in the CONTIG).

                    - Reevaluation of "clipped" sequence regions (see above).
                      Once a sequence has been positioned in a CONTIG, the
                      "clipped" regions can be veiwed and their value
                      reassessed. "Clipped" sequence that is seen to conform
                      convincingly with the aligned sequences of the CONTIG
                      may be "unclipped".

                    - Joining two overlapping CONTIGS. Sometimes the automatic
                      CONTIG assembler will create two separate CONTIGS but
                      also indicate a possible overlap. If the user considers
                      the overlap to be sufficiently convincing, it is
                      possible to join the two CONTIGS "manually".

                    - Complementing a CONTIG. Sometimes required before two
                      CONTIGS can be joined.

                  Checking the accuracy of the CONSENSUS sequences of CONTIGS.

                  Identifying suitable primer sequences within a CONTIG.

                  Tagging and commenting features of interest in a CONTIG.

 13:00 - 14:00    LUNCH

 14:00 - 16:00    Copying of CONSENSUS sequences from a sequencing project
                  database for further analysis.

                  A general look at the analysis of CONSENSUS sequences. It is
                  hoped to make the content of this section reflect the
                  interests declared by course participants in their
                  applications to attend (see above). Possible topics include:

                    - Database searching (BLASTN, FASTA)

                    - Searching for features (coding regions, restriction
                      enzyme sites etc) in the CONSENSUS sequence (NIP).

                    - Comparison of the CONSENSUS seqeunce with related
                      sequences (SIP). Possibly subsequent to a database base
                      search revealing potentially homologous sequences.

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