UniGene
Tabulator 1.1.6
Guide
(Mac OS X version)
Citation:
Lenzi L,
Frabetti F, Facchin F, Casadei R, Vitale L, Canaider S, Carinci P,
Zannotti M, Strippoli P.
UniGene
Tabulator:
a full parser for the UniGene format.
Bioinformatics. 2006 Oct 15;22(20):2570-1.
Epub 2006 Aug 7
INTRODUCTION
This online Guide is designed
for detailed documentation of
UniGene Tabulator 1.1.6 software.
A quick illustrated Tutorial
on how to install the software
and to import the desired UniGene clusters is also available.
--
UniGene Tabulator is a
software solution designed to
manage UniGene biological flat files.
It implements a structured
representation of each UniGene’s format fields,
importing data into a common database managing system,
so it could be used into a local personal computer
(Macintosh and Windows environments).
This database (collection of related tables) enables one to index,
retrieve
or export UniGene information.
More sophisticated functions are possible if one uses FileMaker
Pro 12 or better.
The software minimum
requirements are:
Mac OS X 10.6, OS X Lion
10.7, OS X Mountain Lion 10.8;
Windows XP Professional, Home Edition (Service Pack 3);
Windows Vista Ultimate,
Business, Home Premium (Service Pack 2);
Windows 7 Ultimate, Professional, Home Premium;
Windows 8 Standard and Pro edition.
Download
UniGene_Tabulator 1.1.6 for Mac OS X from address:
http://apollo11.isto.unibo.it/software/
Choose the file: Unigene_Tabulator_Mac.zip
The downloaded file should be automatically decompressed,
generating a "UniGene Tabulator" folder.
Failing this, double
click on the file to activate the default decompression
utility of your system.
The UniGene Tabulator Folder
contains:
"UniGene Tabulator" file
(runtime application);
"UniGene.UGT" (database file);
the "FMP Acknowledgements.pdf" file,
the "Extensions" folder, containing a “Dictionaries” folder,
with the dictionary file for supported
languages;
the "MacOS_Tutorial" and
"MacOS_Guide" folders
contain a copy of the on-line documentation, for
local (off-line) use.
Please do not
change the name of all files and folders
of the "UniGene Tabulator" software.
You may download multiple
copies of "UniGene Tabulator"
and run them simultaneously,
provided that each "UniGene Tabulator" folder is located
in a different directory.
UniGene
Tabulator is based on FileMaker Pro 12 (FileMaker Pro, Inc.)
database management software (http://www.filemaker.com/),
and it released as a FileMaker Pro 12 template,
along with a free runtime application able to run "FileMaker Pro"
at the core of the software.
The UniGene Tabulator solution
imports UniGene “.data”
flat files,
containing cluster information, and ".lib.info" flat files,
containing library
information, into the
database file “UniGene.UGT”.
Choose file for the
desired organism from UniGene ftp server:
ftp://ftp.ncbi.nih.gov/repository/UniGene/.
UniGene Line types/qualifiers in “.data” file
(ftp://ftp.ncbi.nih.gov/repository/UniGene/README):
ID
UniGene
cluster ID
TITLE
Title
for the cluster
GENE
Gene
symbol
CYTOBAND
Cytological band
EXPRESS
Tissues of origin for ESTs in cluster
RESTR_EXPR
Single tissue or development stage contributes
more
than half the total EST frequency for this gene.
GNM_TERMINUS
genomic confirmation of presence of a 3' terminus;
T
if a non-templated polyA tail is found among a cluster's
sequences;
else I if templated As are found in genomic
sequence
or S if a canonical polyA signal is found on the
genomic sequence
LOCUSLINK
LocusLink/EntrezGene identifier associated with at
least
one sequence in this cluster (Hs only)
CHROMOSOME
Chromosome. For plants, CHROMOSOME refers to mapping on
the
arabidopsis genome.
STS STS
NAME=
Name of STS
ACC=
GenBank/EMBL/DDBJ
accession
number of STS
[optional
field]
DSEG=
GDB Dsegment number [optional field]
UNISTS=
identifier
in NCBI's UNISTS database
TXMAP
Transcript
map interval
MARKER=
Marker
found on at least one sequence in this cluster
RHPANEL=
Radiation
Hybrid panel used to place marker
PROTSIM
Protein Similarity data for the sequence with
highest-scoring
protein similarity in this cluster
ORG= Organism
PROTGI=
Sequence GI of protein
PROTID=
Sequence
ID of protein
PCT=
Percent
alignment
ALN=
length
of aligned region (aa)
SCOUNT
Number of sequences in the cluster
SEQUENCE
Sequence
ACC=
GenBank/EMBL/DDBJ
accession
number of sequence
NID=
Unique
nucleotide sequence identifier (gi)
PID=
Unique
protein sequence identifier (used for non-ESTs)
CLONE=
Clone identifier (used for ESTs only)
END=
End
(5'/3') of clone insert read (used for ESTs only)
LID=
Library
ID;
see
Hs.lib.info
for library name and tissue
MGC=
5' CDS-completeness indicator; if
present,
the
clone associated with this sequence is believed
CDS-complete.
A value greater than 511 is the gi of
the
CDS-complete mRNA matched by the EST, otherwise
the
value is an indicator of the reliability of the
test
indicating CDS completeness; higher values
indicate
more reliable CDS-completeness predictions.
SEQTYPE=
Description of the nucleotide sequence.
Possible
values are mRNA, EST and HTC.
TRACE=
The Trace ID of the EST sequence,
as
provided by NCBI Trace Archive
PERIPHERAL=
Indicator
that the sequence is a suboptimal
representative
of the gene
represented by this
cluster.
Peripheral sequences are those that are in
a
cluster which represents a spliced gene without
sharing
a splice junction with any other sequence.
In
many cases, they are unspliced transcripts
originating
from the gene.
//
End of record
UniGene Tabulator software
parses cluster’s data in 5 related tables.
1) “UniGene” is the
master table, it collects the known information about the
transcribed locus – e.g. UniGene cluster identifier, genome
localization
or total number of sequence in the cluster - in a single record.
The master table has a relation “one to many” with each other
table.
2) “SEQUENCE” imports
information about the nucleotidic sequences.
By definition, UniGene clusters are sets of related nucleotidic
sequences,
so there is at least one nucleotidic sequence into a given
cluster.
This table combines information about a sequence
(obtained from both “.data” and “.lib.info” files) in a single
record.
Each cluster will generate in this table a number of record equal
to
its sequence number.
3) “STS” parses each known
sequence tagged sites locate in the transcribed
locus. Each cluster will generate one or more records in this
table.
4) “TXMAP” collects the
“transcript map interval”
retrieved by radiation hybrid analysis.
5) “PROTSIM” retrieves
information about proteins with high similarity with
the peptidic product of the cluster.
Library field qualifiers in “.lib.info” file:
ID=
Library
ID
TITLE=
Title
for the library
TISSUE=
Tissue
used to obtain library
VERBATIM_TISSUE=
Library
tissue,
details
in vertebrates (optional)
DEVELOPMENTAL_STAGE=
Developmental
stage of the library
CANSOURCE=
Cancer
type used to obtain library,
“normal”
if tissue is normal
VERBATIM_DEVELOPMENTAL_STAGE=Developmental
stage
of the library,
details
in vertebrates (optionals)
VECTOR=
Vector
used to obtain the library
UniGene Tabulator software retains data about library
in table “Lib.info_Entries”, information is reformatted to make it
available to table “SEQUENCE” by relationships.
METHOD
First, a detailed
description of UniGene flat file format
(ftp://ftp.ncbi.nih.gov/repository/UniGene/README)
has been accurately analyzed to:
1. identify characters usable
as consistent limits for each data type;
2. convert the flat file
format in a multiple related table series,
allowing the appropriate import for each data type.
Our strategy is based on
importing of the downloaded file.
At the beginning, table
“SEQUENCE”, will collect data from the
“UniGene” file selected.
The lines of UniGene
data file are delimited by line feed “LF”,
so each line will result in a different record.
During this first step, each
UniGene line will be tagged,
according to its starting characters as containing data:
1 about a sequence;
2 about a STS;
3 about transcript map
position;
4 about a similar protein;
5 about cluster’s general
information.
There will be 5 types of line.
The software will maintain data about sequence
(line type 1) in table "SEQUENCE";
sequence data will be parsed into corresponding fields of the same
record,
and these will be correlated to their cluster within the main
table "UniGene".
Information about
sequence tagged site (line type 2) found in clusters
will be parsed in the table "STS";
information about gene map positions by Hybrid Radiation Map
experiments
(line type 3) will be parsed in the table “TXMAP”;
information about known ortholog proteins (line type 4)
will be parsed in the table “PROTSIM”.
In table “SEQUENCE”, which
collects information about cluster sequences,
there are some exceptions:
fields “TISSUE”, “DEV_STAGE”,
“CANCER_SOURCE”, “VERBATIM_TISSUE” and
“VERBATIM_DEVELOPMENTAL_STAGE” are calculated from table
“Lib.info_Entries” by
a relationship, using the key field “LID”;
fields “Lib_TITLE” and
“Lib_VECTOR” are directly visualized from table
“Lib.info_Entries” by the latter relation.
Lines tagged “5” are not
parsed directly.
Firstly, data about the same cluster are joined and only the
complete data
will be parsed in the “UniGene” table, where each bit of information is
extracted from the
appropriate field.
Thus each record into this table collect data from a single
cluster
Table “Lib.info_Data”, which is not
visible,
imports data from “.lib.info” files.
As above, information about a single library
is spread into more than one record.
Like “general cluster information” above,
first library information will be joined,
and only complete data will be parsed
in table “Lib.info_Entries”.
Every step of this
process is driven by a specific FileMaker Pro script,
the software will ask the user when a choice is needed.
Import processes of UniGene data
and Library data are independent
to each other, one can choose to perform both or to import only
UniGene data
and subsequently to import library data.
The first choice will be import library information
before importing
the UniGene file.
The UniGene import process
will clear ALL previously data (parsed and raw),
importing only Library data will delete only library’s data.
In the master file, the main
layout is “UniGene”, from the "Layout menu"
(a pop-up Menu in the top left corner, above the small book icon).
Each record contains fields within a "portal", the FileMaker Pro
tool for
construction of relational databases.
In portals, each field visualizes a field of a related table,
though not all are visualized (to see others fields click on
buttons “Table”,
or choose from the "Layout menu").
--
The free included FM runtime allows free records management and
browsing,
while to create new fields for elaboration or further relationship
definition one need to install the FMP application.
We encourage any
creative use, modification and noncommercial redistribution
of UniGene tabulator, as long as the original paper is cited,
and statement is provided that the original program has been
modified
(in such case).
The availability of
complete UniGene datasets in relational database format
makes for easy integration with other biological databases
available in
the same or similar format; for example: GenBank and EntrezGene.
Each field in each tables
corresponds to a "Feature Qualifier"
accordingly to UniGene Format.
UniGene Tabulator USEFUL FIELDS and field type
descriptions
Table
UniGene:
“CLUSTER”
– Cluster ID (Text field)
“TITLE”
– Cluster title (Text field)
“GENE”
– Gene Symbol (Text field)
“CYTOBAND”
– Cytological band related to
the
expressed locus (Text field)
“GeneID_LID”
– Entrez Gene related
identifier/LocusLink ID
(Number
field)
“HOMOL”
– Presence of known homologue proteins
(Text
field)
“EXPRESS”
– Tissue used to obtain ESTs
(Text field)
“RESTR_EXP”
– Tissue related to more than half of
the ESTs
(Text
field)
“POLY_A”
– Presence of at least an EST
with
Poly
A sequence (Text field)
“CHRO”
– Chromosome related to the expressed
locus
(Number
field)
“SCOUNT”
– Number of total sequence
related to
the
cluster (Number field)
Table
SEQUENCE:
“NACC”
–
Sequence
accession number (Text field)
“CLON”
–
Clone
identifier related to the sequence
(Text
field)
“END”
–
Position
of the sequence referred to clone
(Number
field)
“NUID”
–
Unique
nucleotide sequence identifier (gi)
(Number
field)
“LIBR”
–
Library
ID used to obtain the sequence
(Text
field)
“PUID”
–
Unique
protein sequence identifier
(used
for non-ESTs)
“SEQTYPE”
–
Description
of the nucleotidic sequence
(Text
field)
“TRACE”
–
The
Trace ID of the EST sequence,
as
provided by NCBI Trace Archive (Text field)
“PERIPHERAL”
–
Indicator
that the sequence is a suboptimal
representative
of the gene (Text field)
“TISSUE”
–
Tissue
used to obtain library (Text field)
“DEV_STAGE”
–
Developmental
stage of the tissue used to
obtain
library (Text field)
“CANCER_SOURCE”
–
Descriptions
of the tissue used (Text field)
“VERBATIM_TISSUE”
–
Detailed
description of the tissue for
vertebrate
organisms (Text field)
“VERBATIM_DEVELOPMENTAL_STAGE”
– Detailed description of the developmental
stage
for vertebrate organisms (Text field)
Table
PROTSIM:
“ORG”
–
Organism
of the ortholog protein
(Text
field)
“PROTGI”
–
Sequence
GI of ortholog protein
(Text
field)
“PROTID”
–
Sequence
ID of ortholog protein
(Text
field)
“PCT”
–
Percent
alignment (Number field)
“ALN”
–
Length of aligned region (aa)
(Number
field)
Table STS:
“NAME”
–
Name
of the STS related to a sequence
(Text
field)
“ACC”
–
Genbank
accession number of the STS
(Text
field)
“DSEG”
–
GDB
Dsegment number (Text field)
“UNISTS”
–
Identifier in NCBI's UNISTS database
(Text
field)
Table
TXMAP:
“MARKER”
–
Marker
found on at least one sequence
in
this cluster (Text field)
“RHPANEL”
–
Radiation
Hybrid panel used to place marker
(Text
field)
INSTALLATION
Once decompressed,
UniGene Tabulator can readily be used.
GENERAL DEFINITIONS
File
A set of database tables.
Table
A set of records pertaining
to
the same subject.
Record
One set of fields which
constitute one entry.
The record browser is a small
book icon
at the top left of the window.
You may browse the
database by clicking on the book pages,
or enter a record number and click on the "Return" key.
You
constantly
visualize the following information:
Records: total number of Records in the table
Found: total number of Records currently selected
Sorted: sorting status of the Records
(Sorted/Unsorted)
Field
One area of the record
containing a specific data type.
Browse
Mode
One way to use the database.
It allows data entry, viewing,
browsing, sorting, manipulation.
It may be selected from:
the "View" menu, or
the mode pop-up Menu bar, at the bottom left of the window.
Find
Mode
An alternative way to use the
database.
It allows to search for
specific content in the databases fields,
using any different
combination of criteria
(see the "Search
mode" section below for details about searching).
It may be selected from:
the "View" menu, or
the mode pop-up Menu bar, at the bottom left of the
window.
Preview
Mode
An alternative way to use the
database.
It visualizes a print preview
of the found records.
It may be selected from:
the
"View" menu, or
the
mode pop-up Menu bar, at the bottom left of the window.
Layout
A particular graphical
organization of the field of a table.
A file may show data within
different layouts.
A layout may display fields
from a table or
its related fields from other tables.
Visualization of a field is
independent from the storage of the data contained.
USE
1. Download
UniGene flat files
Download the UniGene
file with the format ".data.gz"
for the organism
desired via ftp at:
ftp://ftp.ncbi.nih.gov/repository/UniGene/
(decompress the files when
appropriate).
Download the corresponding
library information file with the format
".lib.info.gz".
The UniGene page
containing the ftp "UniGene" download link may
also be reached from within the software using the
“Download UniGene data” button.
This invokes the default browser and makes it open a page
containing the “Downlad UniGene” link on the left side blue bar.
Should you be asked for user “Name” and “Password”,
type “anonymous” and your e-mail address, respectively.
At the end of this
step, the user should have two text files
containing cluster data
and library information,
both ready to be imported into the database.
2. Import
UniGene clusters and/or library information.
Different
UniGene
Tabulator databases may be obtained by duplicating
the fresh "UniGene Tabulator" folder and starting new import
sessions.
Records from different database tables may then be exchanged among
different .UGT databases.
IMPORTANT.
Do not import the same text file more than once into
UniGene Tabulator database; download or
decompress the files
again if you need to repeat the import twice.
The
".tab"
text files provided along with the distribution are only
illustratory outputs from the program, and are not intended to be
reimported into UniGene Tabulator, which is designed to import and
parse the original UniGene format data files.
Open the "UniGene tabulator" file into the "UniGene Tabulator"
folder.
Advanced use:
You may open the program files using your copy of FileMaker Pro
8 or later,
thus being fully able to use any modification in the software.
In this case, do not open the program using the "UniGene
Tabulator" file,
but open the file "UniGene.UGT" with your FileMaker.
Following modifications, correct function of the program
requires that
you relaunch it by "UniGene Tabulator" runtime,
due to data pathway structure stored in the “UniGene Tabulator”
scripts.
Click on the "Import UniGene" button.
This starts both importing and parsing of the data.
Select options from the dialog boxes when required.
First, you may choose
if you want to import Library information too.
If you choose “Yes” you will
be asked to select the file “.lib.info”
and then the file “.data”;
if you choose “No” you will be asked to select only the “.data”
file.
You can import library
information later clicking on “Import Library” button.
The time required to
obtain a completely parsed UniGene database mainly
depends on the total cluster number and on the total number of
GenBank sequences composing the clusters. Complete parsing for
large data files
may require up to several days of calculation.
Precomputed databases for Homo
sapiens and Danio
rerio are provided at:
http://apollo11.isto.unibo.it/software/UniGene_Tabulator/
Each field in each table
corresponds to a data type typical of the UniGene Format.
Since Unigene Tabulator 1.1 version:
following parsing of UniGene data
files, the software will create
the UniGene.tab
file within the
'UniGene Tabulator' folder.
3. Use UniGene Tabulator as database.
The FileMaker Pro-based database may be used basically in these
"modes":
"Browse", "Find" and
"Preview".
Switching among different
modes can be obtained from the "View" Menu
or from the pop-up Menu bar at the bottom left of the window.
BROWSE MODE
(“NAVIGATION”)
In the "Browse" mode,
browse of the records set can be made clicking on
the small book icon in the upper left corner, or move up and down between
entry using buttons at the top left of the UniGene layout.
Browse among the tables can be
made clicking on the
“Table” buttons
in the desired section
(Sequence, Protein similarity, STS, Transcript Map).
Alternatively, you can move up and down among the
tables clicking
on the "Layout" pop-up Menu at the upper left corner.
SEARCH MODE (“FIND”)
In the "Find" mode, the
small book icon in the upper left corner
represents different
"requests" that are made for searching in the database.
In the "Find" mode, the user
can fill in a blank form allowing searching
in specific fields.
When searching in the master
table, if one entry contains various recurrences
of a feature, all related records of the respective feature are
displayed.
In FileMaker Pro "Find"
mode, the "AND" - "OR" - "NOT" operators may be used
in this way:
"AND" by filling in different fields located in the
same "Request",
"OR"
by generating additional
requests
(from "Requests" Menu) in the same query,
"NOT" by generating
additional requests (from "Requests" Menu)
and checking the "Omit" box.
The "Symbols" pop-up
Menu in the "Find" mode allows query of
exact matches, ranges,
duplicates, wildcards and more.
The searching results
are entries subsets matching the desired criteria.
PREVIEW MODE
(“PRINT”)
In the "Preview"
mode, one can obtain a print preview of the data
in the actual table.
Browsing among the tables can
be done by clicking on the “Table” buttons
in the desired section
(Sequence, Protein similarity, STS, Transcript Map).
Alternatively, you can move up and down among the
tables by clicking
on the "Layout" pop-up Menu at the upper left corner.
“UniGene
Tabulator” FUNCTIONS AND MENU COMMANDS
UniGene Tabulator MENU
About FileMaker Pro RUNTIMES
Shows information about the
software into a new window.
Preferences
Standard preferences panel, memory can be set up to 256 Mb.
Quit
UniGene Tabulator
Close the program (same as to
click on the red button
on the left upper corner of UniGene window).
FILE MENU
File
Options
In this
application it is possible to set only the "Spelling" option.
Change Password
There is no a default
password.
Page setup
Standard page set-up command.
Print
Standard print command; you
can choose to print:
all
records in the "Found" set, or
only
the current record, or
a
"blank" mask of the record fields.
The appearance will be
that of the layout
currently selected from the layout Menu.
Import Records
This is the general "Import"
function of FileMaker Pro.
Use only "Import UniGene"
function for correct UniGene file import,
from the "Actions" Menu, or clicking on the "Import UniGene" button in
"UniGene tabulator" file.
Export records
Export command for the found
records set in a given table.
Records are exported in their current sorting.
Users can select fields to be
exported, their relative order,
and the separation character.
The option “ALL” will
export all fields (from all tables)
into a Unicode UTF-16 file (default parameters).
Save/Send Record as
An alternative
export function. It export data from the current record,
or the find set of record, into an "Excel" file (.xls).
Send Mail
To send data from each record in the found set by
single e-mail.
Save a Copy as
Save a copy of the database,
complete, compressed or
as clone (database structure
with no record present).
EDIT MENU
Undo
Standard "Undo" command.
Cut
Standard "Cut" text command.
Copy
Standard "Copy" text command.
Paste
Standard "Paste" text command.
Clear
Deletion of selected text.
Select
all
Selection of all the
text within a selected field
(to select a field, click into
the field).
Find/Replace
Utility for search/replace
text strings within fields.
Note: Use "Find" mode (from
"View" Menu)
for full search and selection of a record set.
Spelling
Utility for ceck spelling of
text strings within fields.
Export Field Contents
Utility to export the contents
of the selected field to a file.
VIEW MENU
Browse
Mode
Switch to the "Browse Mode"
(see "General Definitions" above).
Find Mode
Switch to the "Find Mode" (see
"General Definitions" above).
Preview
Mode
Switch to the "Preview Mode"
(see "General Definitions" above).
View as Form
A possible way to display
individually the current record of a
found set of records.
Got to layout
A possible way to switch
between different layout:
UniGene, SEQUENCES, STS, TXMAP, PROTSIM.
View as List
A possible way to display all
the records of a found set as list.
View as Table
A possible way to display all
the records of a found set as
spreadsheet-like table.
Toolbars
To switch on/off the toolbars
of the application: "Standard"
and "Text Formatting".
Status Area
To switch on/off the "Status
Area", the left column toolbar.
Text Ruler
To switch on/off the text
ruler of the application.
Zoom in
To increase layout dimensions,
same as "Zoom +" button.
Zoom out
To decrease layout dimensions,
same as "Zoom -" button.
RECORD MENU
New Record
Create a new empty record in
the database.
The new Record will be the
latest of the current record set.
Duplicate
Record
Duplicate the current record
in the database.
The new Record will be
the latest of the current record set.
Delete Record
Delete the current record in
the database.
Delete All Records
Delete all currently found
records in the database.
Go
to Record
To move to the selected record
by number, previous or next.
Show
All Records
Show all the records in the
database.
Show Omitted Only
Show records in the database
outside of the current found set.
Omit Record
Remove the selected record out
of the current found set,
without deleting it.
Omit Multiple
Remove more then a record,
selected by numbers, out of the current
found set, without deleting them.
Modify
Last Find
Return to the last performed
search to edit it.
Sort Records
Sort the current records set
according to criteria desired.
Unsort
Sort the current records set
according to the order insertion.
Replace Field Contents
Replace the value of a field
into all found set of record with
the value specified in the current record, or by calculation.
Relookup Field Contents
Relookup the value of a field
matching by a the selected key field.
Revert Record
Restore the value of a field,
discard any changes,
before to click out of that field.
ACTIONS
MENU
Import
UniGene
data
Import data from a file in
UniGene flat file format (.data).
(equivalent to the"Import
UniGene" button in the software main
window).
Since Unigene Tabulator 1.1
version:
following parsing of UniGene data
files, the software will create
the UniGene.tab
file within the
'UniGene Tabulator' folder.
This file is a text
tabulated file and contains four columns:
NACC
CLUSTER
GENE
NUID
[GenBank
[UniGene [Gene Symbol] [GenBank
Accession number] Cluster
ID]
GI]
See also:
http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
It could be useful to
readily convert GenBank Accession number into
Gene Symbol, for meta-analysis purposes.
Import Library
info
Import
data from a file in “.lib.info” flat file format.
(equivalent to the "Import
Library" button in
the software main window).
Export From SEQUENCE
This action will export data clustered by ACCESSION NUMBER information,
from the current set of found sequence records
(from all sequence records if no record subset is currently
found).
This action shows two
possibility:
1. All – Each GENBANK
ACCESSION NUMBER will be exported along with all
the related information in a tabulated form
(i.e. all fields presents in the table "SEQUENCE", in this
order:
CLUSTER, TITLE, GENE, CYTOBAND, GeneID_LID, HOMOL,
EXPRESS, RESTR_EXPR,
POLY_A, CHRO, SCOUNT, NACC, CLON, END, NUID, LIBR,
PUID, MGC, SEQTYPE,
TRACE, PERIPHERAL, TISSUE, DEV_STAGE, CANCER_SOURCE,
VERBATIM_TISSUE,
VERBATIM_DEVELOPMENTAL_STAGE);
2. Custom – User can choose
the fields to be exported
(i.e. only selected fields among those described above).
User must choose name
and position of the output file.
The same action starts
clicking on button "Export Sequence" into main layout.
Exporting from other data
tables may be easily performed
choosing the layout of interest, then using the general "Export Record..."
command in the "File" Menu.
Erase
Data
Two possibilities are shown:
1 "Delete raw data": delete
only original raw data about library information.
It may be useful
to "clean" the database following parsing.
Use this
option to reduce the file size.
2 "Delete ALL data": delete
all data in the database tables,
including original flat file raw data and parsed
data.
HELP MENU
About UniGene Tabulator
This command shows information
about the software in a new window.
UniGene
Tabulator
Help
This command
shows the UniGene tabulator tutorial in a new window.
OTHER FUNCTIONS
IN THE MAIN LAYOUT
The mouse pointer is shown as
an hand over the buttons.
Clicking on “Cluster”
word of the title will open
the actual UniGene record for the current cluster,
in the default browser.
Clicking on the arrow
right to “PROTGI” field
in the "Protein similarity" section will open,
in the corresponding
record of the Entrez “Protein” database,
the default browser.
Clicking on the tag of
the “GeneID/LID” field will open,
the corresponding record of the Entrez "Gene” database,
in the default browser.
PROBLEMS
Sometimes, power failure,
hardware problems, or other factors can damage a
FileMaker database file.
When the runtime application
discovers a damaged file, a dialog box appears,
telling the users to contact the creator.
Even if the dialog box does not appear, files can exhibit erratic
behavior.
If you have FileMaker Pro or
Developer installed you can recover it
using the “Recover command”.
Otherwise in Mac OS X
machines, press
Option + while double-clicking the
runtime application icon.
Hold the keys down until you see the open Damage File dialog box.
During the recovery process,
the runtime application:
1. creates a new file;
2. renames any damaged file by
adding “Old” to the end of the filename;
3. gives the repaired file the
original name.
Technical
notes
The scripts at the core of UniGene Tabulator software are
"FileMaker Pro" scripts,
which in part also invoke "AppleScript" language commands.
Bugs report
Please report any suggestion,
bug or problem to:
pierluigi.strippoli@unibo.it