and Import Files
bioLegato File --> Open
menu is "hardwired"
into bioLegato, and can open the main file types that are
the bioLegato program: GDE (.gde), GenBank (.gen), FASTA
interface also has
one or more Import menus, which have been programmed for
that are specific to each bioLegato interface.
File --> Open menu
read files in GDE (.gde), FASTA (.fsa), GenBank
(.gen), or flatfile (.flat) format.
GenBank format - bioLegato can read any file in GenBank
the GenBank release notes from NCBI
originally-read in GenBank format can also be saved as GenBank
because biolegato stores the annotation portion of each
as text, unchanged from the original file.
One word of caution is in order regarding saving in GenBank
a sequence was read in a different format (eg. FASTA)
in a pseudo-GenBank format, in which only minimal annotation
written, since the data for complete annotation does not exist
other file formats. using File
--> SaveAs. However, this
format loses some of the annotation information from the
GenBank file, and in other cases, rearranges data, so that
files generated by bioLegato do NOT comply with the official
- file containing two thionin sequences directly retrieved
read into bioLegato and then saved using SaveAs.
Although the differences between these two formats may
look minor, they
may break programs that read GenBank files. Therefore,
GenBank files using biolegato or dbiolegato, it is
best to save them
directly to a
file, rather than sending them to biolegato and later
GDE format - This format
similar to the ASN.1 format used in
databases. It preserves most of the annotation from the original
- thionin.gen was read into biolegato and then saved using
GDE flatfile format -
This is a
minimal format, which only retains the name and sequence data.
used by biolegato to create temporary files, and there is no way
save to this format.
- bioLegato flat file using thionin sequences from above.
The name of
"sequence" in a GDE flat file indicates the type of data:
bioLegato flat file containing a list of GI numbers for DNA
sequences from Brassica
(TaxID 69183) might look like this:
% - protein
@ - mask sequence
" - text
Foreign Format menu calls readseq,
translate a number of sequence formats into a pseudo-GenBank
The ouput is then read into biolegato. It is important to
other file format contains the complete information found in
files. Usually, only the name of the sequence and the sequence
are retained. Even if this function is used to read in a GenBank
the fact that it is processed by both readseq and biolegato
full annotation may not be retained.
on circular sequences: The only common sequence
file format that
specify whether a sequence is circular or linear is
GenBank. Always use
this format when working with circular sequences.
|The SaveAs menu can be used
save in any of the four formats supported by biolegato.
Export Foreign Format
|The File --> Export Foreign
menu also calls readseq,
to create files in numerous formats. Again, since
biolegato can not
necessarily export all of the original annotation, some
not appear in the exported files.
using thionin sequences from above.
documentation for bltable
|blmarker works with
discrete state data, such as molecular markers. The File --> Import
Phylip Discrete Data menu translates a Phylip
discrete data file
into biolegato flat file, and imports the flat file.
Similarly, the File
Phylip Discrete Data menu saves discrete state
data as a flat
file, which is then translated into a Phylip discrete
Importing Data from a
Molecular marker data is often assembled in a spreadsheet, as
illustrated below. Marker data for each species, isolate, or
should be in a row. The first column is holds tha name of the
isolate or strain, and the remaining columns have the marker
that each column is a different marker (ie. locus).
To use this data in blmarker, it must be saved as a
If you are using StarOffice or OpenOffice Calc,
If you are
using Microsoft Excel
File --> SaveAs
the File Type to
"Text CSV (.csv)".
the field delimiter
is a comma
File --> SaveAs,
- Other formats
- set Save as type to
For example, if your spreadsheet file was MarkerExample.xls,
your data to MarkerExample.csv.
At this point it is a good idea to check your .csv file by
it in a text editor. It should look something like this:
Note: The example above shows that the name
enclosed in quotes. These are okay, as quotes will be
stripped out when the file is read by blmarker.
|To import this file
into blmarker, choose File
Discrete Data from CSV file.
The .csv file is read into blmarker, which should appear
Note: you could also convert a .csv file into a Phylip
file at the Unix
command line using csv2phyl.sh.
|bltree works with
phylogenetic trees. The File
Import Treefile menu translates a Phylip treefile
into biolegato flat text file, and imports the flat file.
Similarly, the File
Treefile menu saves trees in a flat text file,
which is then
translated into a Phylip treefile.