5'_ORF_Extender
Version 2.0.1 (2013)
Tutorial
INDEX
INTRODUCTION
INSTALLATION
SET UP
1. Creation of a local RefSeq mRNA entries
database
1.1.
UniGene data
1.2. Download the RefSeq sequences from UCSC
"Genome Browser"
1.3. Download the RefSeq
data from UCSC "Genome Browser"
2. Creation of a local EST entries database
2.1. Download the EST
data from UCSC "Genome Browser"
2.2. Download the EST sequences from UCSC "Genome
Browser"
3. 5'_ORF_Extender Results
3.1. Download "spliced
EST" information from UCSC "Genome Browser"
3.2. Download "library"
information from UCSC "Genome Browser"
GENERAL DEFINITIONS
4.1 File
4.2 Table
4.3 Record
4.4 Field
4.5 Layout
4.6 Browse Mode
4.7 Find Mode
4.8 Preview Mode
MENU AND COMMANDS
5.1 5'_ORF_Extender
5.2 File
5.3 Edit
5.4 View
5.5 Records
5.6 Scripts
5.7 Help
TROUBLESHOOTING
NOTE - Be sure that
your system default format uses
"." (full stop mark)
as a
decimal separator (English standard).
If
this is not the case, you must change the system
setting.
Mac OS
X: in
"System Preferences" (from the "Apple" Menu),click on
"International", then on "Formats", then choose as
"Region" a country with the English standard format for
numbers (full stop mark as a decimal separator).
System
restart or user logout is not required to make the change
effective.
Windows: in
"Control Panel" (from the "Start" Menu), click on
"International options" then modify the format of numbers
choosing a country with the English standard format for
numbers (full stop mark as a decimal separator).
System
restart or user logout is not required to make the change
effective.
SET UP
1. Creation of a local RefSeq
mRNA entries database (Back
to Index)
In this section, the user is guided to import
RefSeq mRNA genomic coordinates and sequences from UCSC
genome browser into the 'RefSeq_mRNA' table of the software.
In
addition, a table matching each mRNA or EST sequence of
the investigated organism to a genomic locus is imported
following its obtainment from UniGene data.
1.1) UniGene data
To avoid that EST matching a paralogous mRNA are
considered as positive results, the software uses UniGene
data to match each mRNA or EST sequence to a unique genomic
locus.
To
this aim, the user should import the output file of 'UniGene Tabulator'
(version 1.1 or later) software, a tool able to parse the
whole UniGene database for an organism of interest.
Go to the website page:
http://apollo11.isto.unibo.it/software/UniGene_Tabulator/
Your default internet
browser will show the software download page.
Download the current version
of the software for your OS.
Please follow the instructions in the UniGene Tabulator User
Tutorial to automatically parse UniGene data for the
organism of your interest.
Note that for
'5'_ORF_Extender' purpose, it is not necessary to import the
UniGene library data file into UniGene Tabulator.
The parsing process could employ several hours to
complete, depending on the amount of data available for the
selected organism.
The software will create the
'UniGene.tab' file
within the 'UniGene Tabulator' folder. Put this resulting file
into the '5'_ORF_Extender' folder.
1.2)
Downloading the RefSeq sequences from UCSC "Genome Browser"
Go to the website page::
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade: your investigated
clade (e.g.,
Mammal)
genome: your investigated genome
(e.g., Human)
group: "mRNA and EST Tracks"
track: "Human mRNAs"
table: "RefSeq Genes
(refGene)"
region: "genome"
output format:
"sequence"
output file:
RefSeq_Seq.txt
file type returned: gzip
compressed
Click on the 'get
output' button, select 'mRNA' and click on the 'submit' button.
Once the download of the file
'RefSeq_Seq.txt.gz' is complete, decompress it and put the
resulting 'RefSeq_Seq.txt'
file into the '5'_ORF_Extender' folder.
1.3) Dowloading the RefSeq
data from UCSC "Genome Browser"
Go to the website page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade: your investigated
clade (e.g.,
Mammal)
genome: your investigated genome (e.g., Human)
group: "mRNA and EST Tracks"
track: "Human mRNAs"
table: "RefSeq Genes
(refGene)"
region: "genome"
output format:
"selected fields from primary and related tables"
output file:
RefSeq_Data.txt
file type returned: gzip
compressed
Click on the 'get
output' button and select the following fields in the table which appears:
name
chrom
strand
txStart
txEnd
cdsStart
cdsEnd
exonStarts
exonEnds
Click on the 'get output' button at the
bottom of the page.
Once the download of the
file 'RefSeq_Data.txt.gz' is complete, decompress it and put the
resulting 'RefSeq_Data.txt' file into the
'5'_ORF_Extender' folder.
Open the '5'_ORF_Extender'
software.
The yellow buttons will help
to navigate between software tables.
Import the UniGene data and RefSeq data (files
'UniGene.tab', 'RefSeq_Seq.txt'
and 'RefSeq_Data'.txt
located in the '5'_ORF_Extender'
folder) selecting the script "UniGene_and_RefSeq_mRNA_Import" from the "Scripts"
menu and chosing
"Yes" in the window which
appears. The data will be
automatically imported in the appropriate table of the '5'_ORF_Extender' software ('UniGene_ID' and 'RefSeq_mRNA',
respectively) deleting any previously imported data.
Here the RefSeq_mRNA table:
The software will calculate and extract
information for each mRNA record in specific calculated fields of the 'RefSeq_mRNA' table:
FIELD
DESCRIPTION
FIELD "SYMBOLUM":
the gene symbol;
FIELD "UniGene":
it shows "Yes" if a gene symbol
has been assigned to
the mRNA by Unigene;
FIELD "NM_ACCESSION":
the entry GenBank accession number;
FIELD "mRNA_Start":
the genomic coordinate of the mRNA start;
FIELD "mRNA_End":
the genomic
coordinate of the
mRNA end;
FIELD "Strand":
shows "+" or "-" for genome strand, respectively;
FIELD "chr":
the chromosome location;
FIELD "UTR5'_length":
the length of the mRNA 5´ UTR
sequence;
FIELD "Seq_UTR5'":
the mRNA 5´ UTR sequence;
FIELD "Exons_Start":
the genomic
coordinates of the
exons start;
FIELD "Exons_End":
the genomic
coordinates of the
exons end;
FIELD "mRNA_CDS_Start":
the genomic
coordinate of the initiation codon start;
FIELD "mRNA_CDS_End":
the genomic
coordinate of the
stop codon end;
FIELD "bp":
length
of the entry sequence (in bp);
FIELD "Further_Extendable":
shows
"Yes" in the absence
of an in-frame stop codon
upstream
of the described initiation codon in the mRNA
sequence entry;
FIELD "Line":
field
used only during data parsing;
FIELD "FASTA_Line":
the entry in FASTA format;
FIELD "Seq_Line":
the mRNA sequence;
FIELD "Non_NM":
field used during
data parsing to remove non "NM_"
(non-RefSeq) entry
type.
At the end of this
step, the software will have automatically determined which
mRNA is candidate for extension of its 5´ CDS, due to the
absence of an in-frame stop codon upstream of the described
initiation codon in the mRNA sequence entry, and will have
create a list of the EST accession numbers for all ESTs
assigned by UniGene to these mRNAs.
The final output is therefore the creation of the 'EST_List.txt' file in
the '5'_ORF_Extender' folder.
The software also generates a list of RefSeq mRNAs with
a complete CDS (due to the presence of an in-frame stop
codon upstream of the described initiation codon in the mRNA
sequence) by automatically creating the 'RefSeq_mRNAs_with_Complete_ORF.xls'
file in the '5'_ORF_Extender' folder. This file is generated
following selection of the mRNAs whose "Further_Extendable"
field shows "No" and it contains two columns: gene symbol
and mRNA GenBank accession number.
2. Creation
of a local EST entries
database (Back
to Index)
In this
section, the user is guided to download EST genomic
coordinates from UCSC genome browser and to import them into
the 'EST_Data' table of the software.
The EST genomic coordinates are relative to the part of the
EST aligned to the genome by BLAT at UCSC.
User will import these data for the EST assigned to all
mRNAs potentially further extendable at their 5´
CDS, using the file 'EST_List.txt' created in the previous A. step.
2.1) Dowload the EST data from
UCSC "Genome Browser"
Go to the
website page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade:
your investigated clade (e.g., Mammal)
genome:
your investigated genome (e.g., Human)
group:
"mRNA and EST Tracks"
track:
"Human ESTs"
table:
"all_est"
region:
"genome"
identifiers (names/accessions):
click on the 'upload list' button and select the
'EST_List.txt' file created
in the previous
step and located in
the '5'_ORF_Extender' folder
output format:
"selected fields from primary and related tables"
output file:
EST_Data.txt
file type returned:
gzip compressed
Click on the 'get output'
button and select
the following fields in the table which appears:
strand
qName
tStart
tEnd
blockCount
blockSize
qStart
tStart
Click on the 'get
output' button at the bottom of the page.
Once the download of the
file 'EST_Data.txt.gz' is complete, decompress it and put the
resulting 'EST_Data.txt' file into the
'5'_ORF_Extender' folder.
Import this file in the 'EST_Data' table of the '5'_ORF_Extender' software,
by clicking on
the 'EST_Data' yellow button and selecting the script "EST_Data_Import" from the "Scripts"
menu.
The software will calculate and extract
information for each EST record in specific calculated fields of the 'EST_Data' table:
FIELD
DESCRIPTION
FIELD "#EST":
the GenBank accession number of the EST entry;
FIELD "SYMBOLUM":
the gene symbol of the locus to which the EST has been
assigned by the embedded UniGene data table;
FIELD "EST_Start":
genomic start coordinate of the tract of
the EST aligned to
genome by BLAT at UCSC;
FIELD "EST_End":
genomic end coordinate of the tract of the
EST aligned to
genome by BLAT at UCSC;
FIELD "EST_Strand":
shows "+" or "-" for
genome strand, respectively;
FIELD "Block_Count":
the number of EST exons;
FIELD "Block_Size":
the length of each
EST exon;
FIELD "Block_Start_EST":
the coordinate of each exon start in the EST sequence,
relative to the first aligned nucleotide of
the EST;
FIELD "Block_Start_mRNA":
the genomic coordinate of each exon start.
At the end of this
step, the software will have automatically determined
which EST is candidate for extension of its cognate mRNA
5´ CDS, due to the greater extension of the EST sequence
on the genome in comparison with the position of mRNA
5´ end, and will have create a list of the
EST accession numbers for all candidate ESTs.
The final output is therefore the creation of the 'EST_Candidate_List.txt'
file in the '5'_ORF_Extender' folder.
2.2)
Downloading the EST sequences from UCSC "Genome Browser"
In this section, the user
is guided to download from UCSC genome browser sequences of the EST entries candidate to extend
an mRNA 5´ CDS and to import them into the 'EST_Seq' table of
the software.
Go to the
website page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade:
your investigated clade (e.g., Mammal)
genome:
your investigated genome (e.g., Human)
group:
"mRNA and EST Tracks"
track:
"Human ESTs"
table:
"all_est"
region:
"genome"
identifiers (names/accessions):
click on the 'upload list' button and select the
'EST_Candidate_List.txt' file created in the
previous step and
located in the '5'_ORF_Extender'
folder
output format:
"sequence"
output file:
EST_Seq.txt
file type returned:
gzip compressed
Click on the 'get
output' button and select only the following fields in the page which appears (and deselect other fields):
Blocks
One FASTA record per item
All lower case
to lower case
Click on the 'get
sequence' button.
Once the download of the file
'EST_Seq.txt.gz' is complete, decompress it and put the
resulting 'EST_Seq.txt'
file into the '5'_ORF_Extender' folder.
Import this file in the 'EST_Seq' table of the '5'_ORF_Extender' software, by
clicking on the
'EST_Seq' yellow button and selecting the script "EST_Seq_Import" from the "Scripts"
menu.
The software will calculate and extract this
information in specific calculated fields:
FIELD
DESCRIPTION
FIELD "#EST":
the UniGene symbol of the EST
matched entry;
FIELD "bp":
the length of the entry sequence (in bp);
FIELD "Line":
field
used only during data parsing;
FIELD "FASTA_Line":
field used only
during data parsing;
FIELD "Seq_Line":
the EST sequence.
At
the end of this step, the software will have automatically
determined which EST is suitable to extend its cognate mRNA
5´ CDS, due to the presence of a start codon upstream the
mRNA known start codon and in frame with it,
and will have create a list of the EST accession numbers for
all these ESTs.
The final output is therefore the creation of the 'EST_Final_List.txt'
file in the '5'_ORF_Extender' folder.
To visualize the details of the EST
data, including the mRNA 5´ CDS extended sequence when available as a positive
result, switch to the 'EST_Candidate' table by clicking on
the yellow 'EST_Candidate' button:
The software has calculated and extracted this
information for each candidate EST in specific calculated fields:
FIELD
DESCRIPTION
FIELD "SYMBOLUM":
the gene symbol of the locus to which the EST has been
assigned by the embedded
UniGene data table;
FIELD "NM_ACCESSION":
the entry
GenBank accession number of the mRNA to
which the EST has been
matched by the
embedded UniGene
data table;
FIELD "mRNA_Start":
the genomic
coordinate of the
mRNA start;
FIELD "mRNA_End":
the genomic
coordinate of the
mRNA end;
FIELD "Strand":
shows "+" or "-" for genome strand, respectively;
FIELD "chr":
the chromosome location;
FIELD "mRNA_CDS_Start":
the genomic
start coordinate
of the initiation
codon;
FIELD "mRNA_CDS_End":
the genomic end
coordinate of the
stop codon;
FIELD "mRNA_Exons_Start":
the
genomic coordinate of the mRNA exons start;
FIELD "mRNA_Exons_End":
the
genomic coordinate of the mRNA exons end;
FIELD "#EST":
the EST entry genBank
accession number;
FIELD "EST_Start":
genomic start coordinate of the tract
of the EST
aligned to the
genome by BLAT at UCSC;
FIELD "EST_End":
genomic end coordinate of the tract of the EST
aligned to the
genome by BLAT at UCSC;
FIELD "EST_Strand":
shows
"+" or "-" for genomic strand, respectively;
FIELD "Block_Count":
the number of EST exons;
FIELD "Block_Size":
the
length of each EST exon;
FIELD "Block_Start_EST":
the coordinate of each exon start in the EST sequence,
relative to the
first aligned nucleotide of the EST;
FIELD "Block_Start_mRNA":
the coordinate of each exon start in the mRNA
sequence, relative
to the first aligned nucleotide of
the mRNA;
FIELD "Seq_Line":
the
EST sequence;
FIELD "Seq_Line_Reverse":
the
complement EST sequence, calculated if mRNA strand
and EST strand are
discordant;
FIELD "Putative_Extending_Seq":
the
extended sequence from the first EST
genome-aligned
base to the
first EST base just
upstream the
RefSeq mRNA known CDS;
FIELD "Seq_UTR5'":
the mRNA 5´ UTR sequence;
FIELD "UTR5'_length":
the length of the mRNA 5´ UTR
sequence;
FIELD "EST_Candidate":
it
shows "Yes" if the EST is a candidate to extend the
mRNA entry, due to
the presence of a new start codon
upstream the mRNA
known start codon and in frame with
it;
FIELD "Result":
the new extended mRNA 5´ end sequence, when available
as a positive
result, which is the EST sequence
extending from the new first
in-frame ATG codon
to the first
base upstream the RefSeq mRNA known CDS;
FIELD "First_in_frame_ATG":
the position of
the most upstream ATG located in the
EST sequence upstream the RefSeq sequence, which is
in-frame with the start codon
recorded in the
RefSeq
mRNA sequence entry;
FIELD "Completeness":
the EST sequence
containing an mRNA ORF extension is
scanned for the presence of an
in-frame stop codon
upstream of the new initiation
codon identified in the
EST; if it is found, the field
shows "Yes".
3.
5'_ORF_Extender
Results
(Back to Index)
In this section, the user is guided in
downloading sequence information relative to the EST entries
shown above to extend an
mRNA 5´ CDS from UCSC genome browser and
importing them into the 'Results' table of the software.
In particular, this will determine if the EST is classified
as a "spliced EST" and if different ESTs extending the same
mRNA derive from the same library or not.
3.1)
Downloading "spliced EST" information from UCSC "Genome Browser"
Go to the
website page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade:
your investigated clade
(e.g., Mammal)
genome:
your investigated genome
(e.g., Human)
group:
"mRNA and EST Tracks"
track:
"Spliced ESTs"
table:
"intronEst"
region:
"genome"
identifiers (names/accessions):
click on the 'upload list' button and select the
'EST_Final_List.txt' file created in the
previous
step and located
in the '5'_ORF_Extender' folder
output format:
"selected fields from primary
and related tables"
output file:
Spliced.txt
file type returned:
gzip compressed
Click on the 'get
output' button and select the following fields in the table which appears:
qName
qSize
Click on
the 'get output'
button at the bottom of the page.
Once the download of the file
'Spliced.txt.gz' is complete, decompress it and put the
resulting 'Spliced.txt'
file into the '5'_ORF_Extender' folder.
3.2)
Downloading "library" information from UCSC "Genome Browser"
Go to the
website page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
On the web browser page select:
clade:
your investigated clade
(e.g., Mammal)
genome:
your investigated genome
(e.g., Human)
group:
"mRNA and EST Tracks"
track:
"Human ESTs"
table:
"all_est"
region:
"genome"
identifiers (names/accessions):
click on the 'upload list' button and select the
'EST_Final_List.txt' file
created in the previous
step and located
in the '5'_ORF_Extender' folder
output format:
"selected fields from primary
and related tables"
output file:
Library.txt
file type returned:
gzip compressed
Click on the 'get output'
button and select
the following field in the table which appears:
qName
Select gbCdnaInfo from the below list of Linked Tables.
Click on the 'Allow
Selection From Checked Table' button and select the
following field in the table which appears:
library
Click
on the 'get output'
button.
Once the download of the file
'Library.txt.gz' is complete, decompress it and put the
resulting 'Library.txt'
file into the '5'_ORF_Extender' folder.
In the
'5'_ORF_Extender' software, switch to the 'Results' table
by clicking on the yellow 'Results' button.
Select the
"Process_Results" script from the
"Scripts" menu to perform final calculations.
We added several functions which are useful for summarizing
the results, by listing the number of ESTs supporting a
specific extended sequence for each mRNA and the location
(chromosome number) of the mRNA. Calculation of the total
number of genomic loci for which at least one mRNA gives
positive results was also implemented.
At the end of calculations,
the
software has determined various type of information for each
EST extending an mRNA 5´ CDS in the 'Results' table:
FIELDS
DESCRIPTION
"Extended_Loci":
the total number of loci
with extended 5´
coding
sequence;
"SYMBOLUM":
the gene symbol of the locus for which an
mRNA
extension has been
determined ;
"NM_Accession":
the accession number of the
RefSeq mRNA entry
(obtained
from the RefSeq_Parser table);
"UTR5'_length":
the length of the
mRNA 5´ UTR sequence;
"EST#":
the
accession number of the EST sequence assigned to
the same locus
of the RefSeq mRNA sequence entry;
"ATG_position_in_EST": the position of the most
upstream ATG located in the
EST sequence upstream the RefSeq sequence, which is
in-frame with the
start codon recorded in the RefSeq
mRNA sequence
entry;
"Extended_coding_seq":
the new extended mRNA 5´ end sequence, which is the
EST sequence extending from the new
first in-frame ATG
codon to the first base upstream the RefSeq mRNA known
CDS;
"Length":
the length in base pair (bp) of the sequence in the
"Extended_coding_seq" field;
"Media_Length"*:
the medium value of the length
in bp of the new
extended mRNA 5´ end sequence;
"Standard_Deviation_Length"*:
the standard
deviation value of the length in
bp of the sequence in the
"Extended_coding_seq" field;
"Completeness":
the EST sequence containing an
mRNA ORF extension is
scanned for the
presence of an in-frame stop codon
upstream of the new initiation codon
identified in the
EST; if it is found, the field shows
"Yes";
"Extended_EST_per_mRNA":
the
number of the ESTs extending the same mRNA entry;
"Identical_Extension_per_mRNA": the
number of the ESTs with identical sequence
extending the same mRNA
entry;
"Peptide":
the new extended amino terminus amino acid sequence
obtained by
"Extended_coding_seq" field;
"Number_of_aa":
the amino acid
number counted in the "Peptide" field;
"Peptide_length":
the new amino acid
sequence length in "Peptide" field;
"Alert":
it shows "Yes" if the
"Number_of_aa" field is
different from "Peptide length" field, as a
quality
control;
"Chr":
it
shows the chromosome location of the corresponding
entry;
"Spliced_EST":
it shows
"Yes" if the mRNA extension was determined
by
a "spliced EST";
"New_First_Exon":
it shows "Yes" if
the mRNA 5´ end extension reveals
the presence of
a new first exon;
"Second_Exon":
it shows
"Yes" if the EST sequence, extending the mRNA
5´ end sequence, is aligned up to its second
exon;
"Library":
the library accession number;
"Library_Independent":
it shows "No" if more than one EST for
the same
alignment belong
to the same library;
"mRNA_Independent":
it shows "No" if the RefSeq
mRNA CDS is extended by
ESTs all derived
from the same library;
"Transcript_Complete":
the mRNA sequence obtained by piecing
the existing
RefSeq mRNA sequence with
the new extended mRNA 5´ end sequence;
"Transcript_Complete_Length": the length in bp of the
sequence in the
"Transcript_Complete" field;
"Protein_Complete":
the amino acid sequence of
the new
putative
extended
protein;
"Protein_Complete_Length":
the
length in amino acids of the sequence in the
"Protein_Complete"
field;
"Strain":
the mouse strain name from which the EST
sequence was
derived
(obtained from the ESTs GenBank entries).
* = at the bottom of the
page
In addition, the 'Results.xls' file
(that contains all these fields) is automatically created
in the '5'_ORF_Extender' folder.
4. GENERAL DEFINITIONS
(Back to Index)
4.1 File
A set of database tables.
4.2 Table
A set of records referring to the same subject
type (e.g., the 'Genes' table).
4.3. Record
One set of fields which
represent one entry (i.e. containing all requested data for a subject,
e.g. a gene probe).
The record browser is a
small book icon at the top left of the window. You may also
browse the records faster using the cursor at the right of the
small book icon.
4.4.
Field
The database unit containing
a specific data type (e.g., 'Gene_name').
4.5. Layout
A particular graphical organization of the field
of a table.
A table can be visualized
into more than one layout.
A layout may display
fields from a table or its related fields from other tables.
A file may show data within
different layouts.
Visualization of a field
is independent from the storage of the contained data.
Browsing among the layouts
can be made by clicking on the 'Layout:'
pop-up Menu at the upper left corner.
You may browse the
database by clicking on the small book pages at the top left
of the window, or
using the cursor at
the right of the small book icon, or by
entering a record number
and clicking on the "Return" key.
The
following information is constantly displayed on the window
top bar (if not, select "Status
Toolbar" from the "View" Menu):
Records: total number of Records in the table.
Found: total number of the subset of Records
currently selected. Clicking
on the green circular button will retrieve the complementary
subset of currently omitted records.
Sorted: sorting status of the Records
(Sorted/Unsorted).
The FileMaker
Pro-based database may be used basically in these "modes":
'Browse', 'Find',
and 'Preview'.
Switching among different
modes can be done from the 'View'
Menu or from the
pop-up Menu bar at the bottom left of the window.
4.6 Browse Mode
One way to use the database.
It allows entry, view, browse, sort, and manipulation of
data.
It may be selected from:
the 'View' menu, or
the pop-up mode Menu bar, at the bottom left of the
window.
In the 'Browse' mode, the record sets can be
browsed by
clicking on the small book icon (with the arrows to move
'back' and 'forward') in the upper left corner.
Browsing among the tables can be done by clicking
on the 'Layout'
pop-up Menu at the upper left corner.
4.7 Find Mode
An alternative mode to use the database.
It allows searching for
specific content in the database fields, using any different
combination of criteria
(see the 'Search mode'
section below for more details).
It may be selected from:
the 'View' menu, or
the mode pop-up Menu bar, at the bottom left of the
window.
The user can fill a blank form
allowing to search
in specific fields.
In the "Find" mode, the small
book icon in the upper left corner represents different
"requests" that are made for searching the database.
In FileMaker Pro 'Find'
mode, the "AND" - "OR" - "NOT" operators may be implemented in this way:
"AND" by filling criteria
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
clicking
on the "Omit"
button (located on the top bar
in the window).
The 'Operators' pop-up Menu
appears by clicking on a field while pressing the 'ctrl' key, allowing query
of:
exact matches, duplicate
values, ranges, wild cards and more.
Click on the 'Perform Find'
button at the top of the window to start the query.
The result of the search
is the subset of the entries matching the set search criteria.
4.8 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 pop-up Menu bar, at the bottom left of the
window.
In the "Preview" mode, the
user can obtain a print preview of the data in the current table.
Browsing among the tables
can be done by clicking on the 'Layout:' pop-up Menu at the upper left corner.
5. MENU AND COMMANDS
(Back to Index)
5.1 "5'_ORF_Extender"
Menu
(Back
to Index)
About FileMaker Pro Runtime...
Information about
FileMaker Pro Runtime at the core of the software.
Preferences...
Standard preferences
panel; cache memory size can be set at up to 256 Mb.
Hide
5'_ORF_Extender
Hiding all 5'_ORF_Extender windows.
Quit
5'_ORF_Extender
Closing the program.
5.2 'File'
Menu
(Back to Index)
File Options...
It is possible to set only
the "Spelling" options.
Change
Password...
There is no default
password set.
Page
setup...
Standard page set up
command.
Print...
Standard print command.
The appearance will match
the layout
currently displayed on the screen.
Import
Records
This is the general
"Import" function of FileMaker Pro.
Export
Records...
Export command for the found records set in a
given table.
Records are exported in
their current sorting mode.
User can select fields
to be exported, their relative order,
and the separation
character.
Save a
Copy as...
Save a copy of the database, complete,
compressed or
as a clone (database structure with no record present).
5.3 'Edit'
Menu
(Back to Index)
Undo
Standard "Undo" command.
Cut
Standard "Cut" text command.
Copy
Standard "Copy" text
command.
Paste
Standard "Paste" text
command.
Select
all
Selection of all text
present within a selected field
(to select a field, click
into the field).
Find/Replace
Utility for
searching/replacing text strings within fields.
Note: Use 'Find' mode (from
'View' Menu)
for
full search and selection of a record set.
Spelling
Function for checking
spelling of text strings within fields.
Export
Field Contents...
Function for exporting
the contents of the selected field to a file.
5.4 'View'
Menu
(Back to Index)
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).
Go to
layout
A possible way to switch
between different layouts.
View
as Form
A possible way to individually display the current record
of a found set
of records.
View
as List
A possible way to
display all the records of a found set in the form of a
list.
View
as Table
A possible way to
display all the records of a found set in the form of a 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 toolbar located at the top of the program
window.
Text
Ruler
To switch on/off the
text ruler of the application.
Zoom
in
Used to increase layout
dimensions.
Zoom
out
Used to decrease layout
dimensions.
5.5
'Records' Menu
(Back to Index)
New
Record
Creating a new empty
record in the database.
The new Record will be the
latest of the current record set.
Duplicate
Record
Duplicating the current
record in the database.
The new Record will be the
latest of the current record set.
Delete
Record...
Deleting the current
record in the database.
Delete
Found Records...
Deleting all currently
found records in the database.
Go to
Record
Moving to the selected
record by number, previous or next.
Show
All Records
Showing all the records in
the database.
Show
Omitted Only
Showing all the records in
the database not included in the current 'found' set.
Omit
Record
Removing the selected
record out of the current found set, without deleting it.
Omit
Multiple...
Removing more than a
record, selected by numbers, out of the current found set, without deleting
them.
Modify
Last Find
Returning to the last
performed search in order to edit it.
Saved
Finds
Saving a set of search
criteria.
Sort
Records...
Sorting the current
records set according to desired criteria.
Unsort
Display the current
records set according to the order of creation of each record.
Replace
Field Contents
Replace the value of a
field into all found set of records with the value specified in the
current record, or by calculation.
Relookup
Field Contents...
This command executes a
relook up of the value of a field by reading the matched value
in a related table (the relationship has been established
during database development using a 'key' field).
Revert
Record...
Restoring the value of a
field, discarding any change, before clicking out of that field.
5.6 'Scripts'
Menu
(Back to Index)
About
This opens the 'About'
window containing information about the 5'_ORF_Extender software.
Guide
The page with the user Guide
of the 5'_ORF_Extender software (this Guide).
5.7
'Help' Menu
(Back to Index)
Search
Search a system 'Help' for
the general commands.
TROUBLESHOOTING
(Back to Index)
Sometimes, power failure,
hardware problems, or other factors can damage a FileMaker Pro database file.
When the runtime
application discovers a damaged file, a dialog box appears, prompting the user to contact
the creator.
Even if the dialog box
does not appear, files can exhibit erratic behaviour.
If you have FileMaker Pro
or FileMaker Pro
Advanced
installed you can recover it using the 'Recover' command.
Otherwise, to recover a damaged file:
- On Mac OS X machines,
press Command + Option (cmd-alt) while double-clicking the runtime application icon. Hold the keys down until you
see the 'Open Damaged File' dialog box.
- On Windows
machines, press Ctrl+Shift while double-clicking the runtime
application icon. Hold the keys down until you see the Open
Damaged 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
file name;
3. Gives the repaired file
the original name.