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Dnaman Sequence Analysis Software

This document describes the sequence editing features of the DNAMAN sequence analysis software. It allows users to retrieve sequences from online databases or enter custom sequences, load existing sequences, define sequence properties, display and convert sequences, and generate random sequences from existing sequences or templates. The software supports common sequence formats and can export sequences in multiple formats.

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kamal
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426 views17 pages

Dnaman Sequence Analysis Software

This document describes the sequence editing features of the DNAMAN sequence analysis software. It allows users to retrieve sequences from online databases or enter custom sequences, load existing sequences, define sequence properties, display and convert sequences, and generate random sequences from existing sequences or templates. The software supports common sequence formats and can export sequences in multiple formats.

Uploaded by

kamal
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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DNAMAN

Sequence Analysis Software

Sequence
Editing

BIOINFORMATICS PLATFORM
Sequence Editing Features
 Retrieve Sequence From the Internet
 DNAMAN Sequence Format
 Enter Custom Sequence
 Load Existing Sequence
 Analysis Definition
 Work with other Sequence Formats
 Show/Convert Sequence
 Generate Random Sequences
Retrieve Sequence
From the Internet
1. Type ncbi.nlm.nih.gov in browser bar
2. Select Nucleotide
3. Type pUC18 and Press Search button

2 3

1
Retrieve Sequence
From the Internet
1. Click pUC18 link to open sequence
2. Click Send to
3. Choose Destination to File
4. Choose GenBank format and click Create File button

2
3

4
1
Retrieve Sequence
From the Internet
1. Click Save button to download file
2. Enter file name to save
3. Click Open button after file saved
1

3
Retrieve Sequence
From the Internet
Sequence is loaded into DNAMAN
DNAMAN Sequence
Format
 DNAMAN uses simplified GenBank Format
 GenBank file is automatically recognized in DNAMAN
 “FEATURES” in GenBank file are parsed out as
annotations in DNAMAN
 Sequence contents begin after Keyword “ORIGIN”
 Sequence name is labeled after keyword “Locus” or
“Seq”
 Keywords “REFERENCES” and “SOURCES” can be
stored in sequence databases, bit not used in
Sequence Analysis
Enter Custom Sequence
1 Enter Sequence Manually
4 1. Choose File menu and click
New file
2. In Text Window, type Seq and
follow with sequence name
3. Type ORIGIN then enter
sequence contents
2 4. Save the sequence file
3
Load Existing Sequence

From File | Open menu


 Click File | Open menu
 Browse the computer to find sequence files
 Click the file to open
 DNAMAN loads automatically the sequence to channel for
analysis

From File Control


 Click the File tab in Sequence Controls on the left of workspace
 Browse the computer directly from the File control
 Click the file to open
 DNAMAN loads automatically the sequence to channel for
analysis
Analysis Definition
1 After Sequence Loaded in Channel
1. Click Define Sequence on
Ribbon bar or Channel control
2. Analysis Definition Dialog box
1 shows up
2
Analysis Definition

1 2 3 5

4 6
7
8

Sequence Analysis Definition


1. Change sequence name
2. Toggle Linear/Circular DNA sequence
3. Toggle DNA/Protein sequence
4. Define analysis region if only partial sequence is subject to analysis
5. Reset analysis positions if analysis region defined
6. Rotate sequence origin for circular DNA
7. Edit annotations
8. Export/Import annotations or sequence content
Work with other Sequence
Formats
DNAMAN Reads Files
DNAMAN Exports Files
 GenBank
 FASTA (Single and multiple
 FASTA (Single and multiple
alignment) alignment)
 Trace files: ABI and SCF  GFF3
 GFF3  GCG multiple alignment
 GCG multiple alignment (aln)
 GDE multiple alignment
 GDE multiple alignment
 CLUSTAL multiple alignment
 CLUSTAL multiple alignment
 NBRF multiple alignment  NBRF multiple alignment
 PHYLIP multiple alignment  PHYLIP multiple alignment
 MEGA multiple alignment
Show/Convert Sequence
1
After Sequence Loaded in Channel
2 1. Click Sequence tab in Ribbon
bar
3 2. Click Display in Sequence Data
section
3. Display Sequence box shows
up
6 4. Choose type of sequence to
display
5 5. Choose how annotations to be
4 shown
6. Choose what annotations to
show/hide
Show/Convert Sequence
Display Results
Random Sequence
1 1. Click Sequence tab in Ribbon
bar
2. Click Random in Sequence
2 Data section
3 3. Random Sequence Generator
box shows up
4. Choose type of sequence
4 5 5. Choose fragment size
6 6. Choose a sequence template
for composition if needed
7 7. Modify composition if needed
Random Sequence
Randomize Current Sequence
1 After Sequence loaded in channel
1. Click Sequence tab in Ribbon
bar
2. Click Random Arrow in
2, 3 Sequence Data section
3. Choose Current Sequence
4 menu
4. A randomized sequence shows
up
Random Sequence
Fragment Current Sequence
1 After Sequence loaded in channel
1. Click Sequence tab in Ribbon
bar
2. Click Random Tool in Sequence
2, 3 Data section
3. Choose Fragmentation menu
4 4. Enter parameters to generate
fragments of the current
sequence
All fragments in random sizes and
positions from the sequence show
up in a Text window.

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