This BioCompanion copy is a demo version .
This section describes the methods available to enter a sequence into the computer by manual
typing. The automatic import of existing data files has been described
in the reformatting chapter . The use of programs in the GCG package as described in this
section requires that the setup of the GCG software
has been completed. Within Seqlab, sequence editing bacame rather easy. If you insist on character-based
editing, use the seqed program as supported in previois versions of GCG. If
you have the sequence in electronic form already but did not use it in GCG before, refer to the
previous chapters for details.
Before the genomic sequencing age, sequences had always to be typed in. Today,
the automatic sequencing has frequently obsoleted the manual procedures. Once
you obtained the four nucleotides as chromatogram, a totally different informatics aspect applies
(also referred to as Lab automation software). Besides the software which is typically supplied
with the sequenator machine, various PC- and Mac based programs as well as UNIX-based software
have been established. Today's pressure on economic sequencing has raised the necessity to obtain
as long reads as possible. Therefore, the basecalling and the assignment of
sequence reads from the traces has become a major element in processing. Assuming
that the traces are available in binary format, there are several packages you might be interested
in using: It is well understood that you do no longer obtain your desired sequence in a single run,
but frequently need to assemble the obtained sequence fragments from several fragments into so-called
contigs . GCG's approach to the fragment
assembly is described below. The following section focuses on the creation
of new sequences . If you have already created a contig with any of the software packages
above, refer to the section on sequence import for details
how to proceed. This chapter also contains a section on SeqLab's way to handle
sequences.
In order to type in sequences , you might want to use a different program
to type in sequences, such as text editors or PC-based software. GCG's 'SeqLab' program runs
on the Bioinformatics compute resource computer and, therefore, is only one of your options.
If you choose a different environment, make sure that
the sequences are either following GCG format
conventions or may be reformatted to this format
easily. PC users might also want to ensure that the infrastructure to
transfer or share
files is well established. Refer to the hints on
public domain software for considerations on the implementation of non-standard software.
Keep in mind to enter data in a fashion that allows others (and yourself) to identify the
sequence and its features. It is essential to keep in mind that a sequence entered by yourself
has all major features added properly, such as a database
entry : The annotation of such a sequence is quite important and should not be underestimated.
The annotation of newly generated sequences for submission to the databases is best achieved
by using the WWW driven input tools as available on the WWW servers from EBI, DDBJ and NCBI.
The users of automatic sequencing machines has already been mentioned above.
You will most probably want to use software delivered with the machine in order to convert the
traces of base pairs into DNA sequences. Alternatives have been mentioned above as well.
The last section of this chapter describes the Fragment Assembly
System (FAS) used to assemble sequence fragments which
have been entered before into larger contigs .
The Seqlab software has a different way to handle, and edit, sequences and is
described below .
[next page] , or [overview] , or [table of contents] Considerations
The Place Of Birth Changed
Use of programs other than the GCG package
Entering Data Is Serious
Related Programs
JAMF source file: enter.jam
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