[转发]DNAMAN使用手册(An Integrated System for Sequence Analysis)

Sequence Manipulation
Sequence input
Information exchange
Editing
Sequence composition and conversion
BLAST documents

Sequence input

DNAMAN provides 20 sequence channels to keep active  sequences in memory. These sequence channels simplify
multiple functional analyses and substantially increase the efficiency of your works. A panel window shows the current working sequence. You may edit the sequence directly in the panel.

Information exchange
DNAMAN accepts sequence files in GenBank, GCG, CUSTAL, FASTA, PIR and GDE format. It can export multiple sequences in GCG, CUSTAL, PIR and GDE format.DNAMAN provides a word processor for sequence editing. With this word processor, you can incorporate charts, images, graphics from any other Windows software into your documents.DNAMAN works as an object linking and embedding (OLE) server to exchange the information of restriction maps with other software. With OLE, you can incorporate your restriction maps into other Windows applications, and directly modify the maps within the applications
Editing
Editing a text file with DNAMAN is as easy as working with your favorite word processor. With the word processor of DNAMAN, you can edit original sequence files, and the analysis results as well.

Sequence composition and conversion
DNAMAN reports the composition and molecular weight of a sequence.It performs the conversion of a sequence to its reverse, complementary, reverse complementary, double strand, and RNA sequences

BLAST documents
In addition to accessing the Internet through Web browser, DNAMAN prepares a file in BLAST document formats with a query sequence for directly accessing BLAST E-mail Server. Five BLAST document formats are currently available: Blastn, Blastx, Tblastx, Blastp and Tblastn.

Examples:

Internet/Intranet Browser
  
DNAMAN provides an integrated Web browser  to access to the Internet or your Intranet.

You may load sequence from the brwoser for direct analysis.

You may also work with the servers on the Internet.

Sequence Search
Search for nucleotide sequences
Search for consensus sequences
Search for open reading frames
Search for repeat sequences
Search for amino acid sequences

Search for nucleotide sequences
With DNAMAN, you can search for nucleotide sequences from one or both strands of a DNA sequence. Gaps and ambiguous nucleotides are allowed in the query sequences. You may search for a list of query sequences on the target sequence.


DNAMAN instantly reports the searching results in graphics. Colors and arrowheads indicate different sequence groups and sites. You may magnify any region of the DNA fragment and display the regional sequence of by selection.

Search for consensus sequences
With DNAMAN, you can search for DNA or protein consensus sequences from both strands or six reading frames of DNA sequences. DNAMAN provides a database of DNA and protein consensus sequences. The database is expandable and editable. You can create custom consensus sequence databases.

Search for open reading frames
You may search for open reading frames from six reading frames of a DNA sequence. The searching results are shown in a text table. DNAMAN also provides a graphical view of the location of Start/Stop codons on a DNA sequence.

Search for repeat sequences
You may search for direct repeat and reverse repeat sequences from both stands of a DNA sequence. You can also search for reverse complementary repeat sequences that may form hairpin/stem-loop structures.

Search for amino acid sequences
You may search for an amino acid sequence and its variations from the six reading frames of a DNA sequence. DNAMAN allows ambiguous amino acids as well as a number of mismatches in a query sequence

Restriction Analysis
Restriction site analysis
Restriction map
Restriction pattern illustration
Electronic cloning
Constructing restriction maps
Silent mutation
Directed mismatch

Restriction site analysis
You can search any restriction site on a DNA sequence. DNAMAN supplies two restriction enzyme files; the restrict.enz file with 180 most frequently used restriction enzymes, and the dnamanre.enz file with 1364 enzyme records. You can also create your own enzyme files. All the enzyme files are editable and expandable.

DNAMAN provides custom restriction enzyme filters on cutter, ends, frequency and methylation sensitivity. Users can define the DNA molecule as a linear or a circular type.

DNAMAN reports the restriction analysis results in an easy-to-read table. The cutting sites are shown in alphabetical order of enzymes, and in site position order as well. The non-cutting enzymes are also listed. In addition, DNAMAN displays enzyme sites on the top of the DNA sequence.

Restriction map
DNAMAN provides easy-to-use tools to produce publication-quality restriction maps. These tools can be used to draw linear or circular restriction maps with or without DNA sequence information. You can also draw maps for other projects, such as PCR strategy diagrams, gene structural maps, etc.

DNAMAN accompanies with a high quality drawing program, LBDraw. Working with LBDraw, you can easily make sophisticated diagrams with many restriction maps.

Restriction pattern illustration
DNAMAN predicts the patterns of restriction enzyme digested DNA fragments in a gel electrophoresis. You can perform single enzyme digestion on multiple sequences, and single or multiple digestion on a single sequence. DNAMAN shows the information of restriction fragments on their sizes and ends when you click on these fragments.

Electronic cloning
DNA cloning is a time consuming and expensive process. DNAMAN provides easy-to-use tools to design a cloning strategy and performs evaluation analyses on target sequences. This feature could improve the efficiency of your cloning work in laboratory.

DNAMAN mimics basic steps of the actual cloning process: Restriction analysis on the original vector and insert sequences Selection of vector and insert fragments from restriction pattern Verification of the end compatibility of DNA fragments Modification of fragment ends if necessary Insertion of linkers if necessary Producing the final clone sequence

Constructing restriction maps
DNAMAN can help you reconstruct a restriction map in the absence of DNA sequence. You must provide all fragment sizes in single and double digestion. DNAMAN deduces the possible restriction map(s) from the information of restriction fragments.

Silent mutation analysis
Silent mutation analysis allows you to design a desired mutation site on a DNA sequence. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches for potential mutation positions to create or destroy restriction enzyme sites.

Directed mismatch analysis
Directed mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating a single or double mismatch at a site near the mutation. Using this function you can create or destroy a restriction site in order to distinguish the wild type allele and a common mutant allele.

Sequence Assembly
Sequence assembly method
Sequence assembly editor

Sequence assembly method
DNAMAN uses fast alignment algorithms to assemble quickly and accurately a large number of overlapping sequences. DNAMAN can automatically adjust the orientation of each fragment and remove vector sequences as well. You can set sensitivity parameters to control gaps and ambiguous sequences in contigs.

Sequence assembly editor
DNAMAN displays sequence assembly project in three windows: Graphic window provides an overview of the assembly construction. You can edit this graphical presentation to produce high quality diagrams for publications.

Name list window contains all assembled sequence names. You can change the sequence order by moving the sequence names in this window.

Sequence window shows all original sequences and a consensus sequence. You can edit any of the original sequences to improve the result of sequence assembly.

DNAMAN exports sequence the assembly result in a text window. You have options of reporting the consensus sequence only, or all sequences including the consensus sequence and original sequences.

Sequence Homology Analyses
Dot matrix plot
Two sequence alignment

Dot matrix plot
With DNAMAN, you may compare two DNA sequences or two protein sequences in a dot matrix plot. A specific algorithm is developed to yield high quality dot matrix plot. With this method, long DNA sequences can be compared in short time with little background noise. You may efficiently compare genomic sequence with the dot-matrix plot function of DNAMAN.

DNAMAN displays the actual sequences and their alignment on any selected region in a sequence window.

Two sequence alignment
DNAMAN uses fast or optimal algorithms to align two DNA or protein sequences. You have options to control the sensitivity of alignment. DNAMAN also allows you to select any region of target sequences for alignment.

For DNA sequence alignment, you have an option to use the minus strand for comparison. For protein sequence alignment, DNAMAN can report the amino acid similarity of two protein sequences in a text window. The amino acid similarity matrix is editable by users.

Multiple Sequence Alignment
Multiple sequence alignment methods
Multiple sequence alignment editor
Multiple sequence input and output
Phylogenetic trees
Restriction analysis
Hydrophobic / hydrophilic profile
Secondary structure prediction

Multiple sequence alignment methods
Algorithms
DNAMAN uses ClustalW algorithm (Feng-Doolittle and Thompson) for Optimal Alignment, and the global alignment algorithm (Wilbur and Lipman) for fast alignment. The three types of Optimal Alignment in DNAMAN provide high quality alignment results. With the Fast Alignment method, you may quickly align a large number of DNA or protein sequences.

Parameters and Methods
You may set different parameters to make adequate alignment for your DNA or protein sequences. The multiple alignment function of DNAMAN is threaded. You may run up to 16 sets of multiple alignment simultaneously. You may also perform other sequence analysis while doing the multiple alignment.

Multiple sequence alignment editor
DNAMAN provides a high performance alignment editor. A graphical view of the alignment allows you to quickly move to an interesting region. You can change the alignment list order by drag and drop sequence names. You are also able to add or delete gap insertions, move a fragment within a gap and truncate aligned sequences

You can modify the appearance of multiple alignment sequences:
displaying identical residues in colors or blocks
displaying consensus sequence
changing text font

Multiple alignment input and output
You can directly input sequences or multiple alignment profiles for alignment from the following sources: GenBank, EMBL/Swiss Prot, GCG/MSF, CLUSTAL, FASTA, NBRF/PIR GDE The multiple alignment editor can output an alignment in different formats: GCG/MSF, CLUSTAL, NBRF/PIR, and GDE. The multiple input and out put capacity of DNAMAN makes it compatible with major sequence analysis software.

Phylogenetic trees
DNAMAN calculates the homology matrix and establishes related distances between all pairs of sequences. Consequently, DNAMAN can output a distance matrix of multiple alignment, and draw phylogenetic trees or homology trees. You can carry out bootstrapping tests for the confidence value of a phylogenetic tree.

Restriction analysis
If the sequences in multiple alignment editor are DNA, you can perform a restriction analysis on these sequences. This analysis is useful in restriction site comparison of aligned DNA sequences.

Hydrophobic / hydrophilic profiles
If the sequences in multiple alignment editor are protein, you can plot the hydrophobic or hydrophilic profile of all sequences for comparison.

Protein secondary structure prediction
DNAMAN predicts the secondary structure of multiple protein sequences using the DSC method developed by King and Sternberg.

Primer Analysis
Primer design
Melting temperature prediction
Complementarity of primers
Mispriming analysis
Silent mutation primers
Directed mismatch primers

Primer design
The function of primer design includes not only primer filtration by Tm, but also mispriming and restriction analyses on the primers. DNAMAN can help you to find optimal primers that satisfy your requirements.

DNAMAN allows you to set numerous control criteria for optimal primer filtration, such as the regions of target DNA, size of PCR products, primer characteristics, reaction conditions and primer configurations.

You can carry out a restriction analysis on the primers in order to select those with or without restriction site(s). You can discard the primers that are easy to anneal to secondary sites of target DNA using mispriming analysis.

Melting temperature prediction
DNAMAN calculates and reports the thermodynamic Tm, hybridization Tm, and GC+AT Tm of DNA-DNA hybridization. You can also have the Tm information on the hybridization of DNA-RNA and RNA-RNA. These Tms can be used for PCR primers as well as hybridization probes.

Complementarity of primers
Primer complementarity may affect the performance of PCR primers or hybridization probes. DNAMAN analyzes the following three kinds of primer complementarity.

Self-complementary
DNAMAN searches for the most possible self-complementary configuration of primers with the lowest free energy. Complementarity with target DNA DNAMAN searches for the complementary sequences between the primer and both stands of target DNA. Two primer complementarity DNAMAN searches for complementary sequences between two primers. It reports the continuous and discontinuous complementary sequences.

Mispriming analysis
With mispriming analysis you can search for all possible annealing sites of a primer on target DNA sequence. DNAMAN allows you to set up Score matrix: perfect match, mismatch and G-T match; Position weight matrix, Gap penalty and Cut-off score. This analysis can eliminate PCR primers that are easy to anneal to secondary sites.

Silent mutation primers
Silent mutation analysis allows you to design a desired mutation site on a DNA sequence. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches for potential mutation positions to create or destroy restriction enzyme sites. You can use this function to design primers to create a silent muation on target DNA sequence.

Directed mismatch primers
Directed mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating mismatch at a site near the mutation. Using this function you can design PCR primers to create or destroy a restriction site in order to distinguish the wild type allele and a common mutant allele.

Translation and Protein Analysis
Translation
Genetic code table
Reading frame overview
Codon usage analysis
Amino acid composition
Protein hydrophobic and hydrophilic profile
Protein charge and pI analysis
Protein secondary structure prediction
Reverse translation

Translation
DNAMAN deduces protein sequences from three reading frames of a DNA sequence and displays results with many options. By setting the number of amino acid per one line, you can change the layout of the translation file.

DNAMAN allows you to select any region from a sequence file, and perform translation analysis. In the report file DNAMAN shows both translated and untranslated regions.

Genetic code table
DNAMAN provides seven genetic code tables with the options of adding new code tables or editing any existing one. You may select any genetic code table for translation and protein analysis.

Reading frame overview
DNAMAN presents a graphical overview on six reading frames of a DNA sequence. It is a useful feature to locate the ORFs on a large DNA sequence.

Codon usage analysis
DNAMAN provides a codon usage table for any reading frame of a DNA sequence. The table indicates the number and frequency of each codon used in a reading frame.

Amino acid composition
DNAMAN reports the amino acid composition, pI and molecular weight of a protein sequence.

Protein hydrophobic and hydrophilic profile
DNAMAN shows protein hydrophobic and hydrophilic profiles in a graphic window that may help you to predict hydrophobic clusters or antigen regions in a protein sequence. The graphical profiles are editable to produce high quality illustrations for publications.

Protein charge and pI analysis
DNAMAN calculates protein charge at a given pH. It shows also the predicted isoelectric point of the protein. In addition, DNAMAN can deduce the suitable buffer pH for a desired charge.

Protein secondary structure prediction
DNAMAN predicts the secondary structure of a protein sequence using the DSC method developed by King and Sternberg.

Reverse translation
DNAMAN provides the reverse translation of a protein sequence. It reports the reverse translated DNA sequence with ambiguous nucleotides at variant positions. This feature can be used to degenerate primers from peptide sequences.

Database Management
Oligo database
DNA and protein database
Searching in DNA or protein database

Oligo database
You may have a large number of oligo nucleotides for experiments of sequencing, blotting, PCR, etc....DNAMAN provides an oligo database manager that can help you to effectively organize and use these oligoes.

When you create oligo databases for different projects. DNAMAN allows you to attach a password for the security of the database.

Any oligo database is expandable and all records are editable. You can provide information for each record in seven fields: name, source, memo, length, GC content, melting temperature and sequence. The name, source, memo, length can be used as sorting keys. You can import a large number of oligo records from a text file, or export any record to a text file.

DNA and protein database
DNAMAN database manager is used to collect and store DNA and protein sequences. You can create or delete a DNA or protein database and set security to protect the database.

DNAMAN has an easy-to-use database manager. All databases are expandable and all records are editable. You can directly import records from text files, GCG and GenBank files. The information related to any record is shown in seven fields: sequence name, definition, keywords, source, reference, memo, coding region. The first four fields can be used as sorting keys.

Searching in DNA or protein database

You may search for homology sequences of a target DNA by scanning all records in a DNA database. The algorithm for the comparison is fast alignment method. You may search for a nucleotide sequence from both strands of all records in a DNA database. You may search for a peptide sequence from all records of a protein database as well as the six reading frames of all records in a DNA database.

LBdraw: Designed for Molecular Biologists

Features of LBDraw

What LBDraw does
Communication with DNAMAN
Standard drawing tools
Drawing tools for molecular biologists

What LBDraw does
LBDraw is a Windows drawing program. It is designed to draw and assemble drawing objects. It provides not only standard drawing tools, such as rectangle and ellipse tools, but also the tools designed for molecular biologists, such as double strand DNA structure and virus tools. LBDraw is an OLE server and client application, which means you can incorporate objects of any other OLE server programs into LBDraw and deliver LBDraw objects to other OLE client applications. This is especially useful to draw diagrams in molecular biology.

Communication with DNAMAN
DNAMAN is an OLE server of the restriction map object. When you insert a restriction map of DNAMAN into a LBDraw document, you can edit the map directly in the document with the DNAMAN editing tools.

The word processor (Text Editor) of DNAMAN is an OLE client. You can insert the drawings of LBDraw into the word processor. You are also able to edit the drawings in DNAMAN with the drawing tools of LBDraw.

Standard drawing tools
LBDraw provides the following standard drawing tools: Text, Straight Line, Arrow Straight Line, Multiple Line, Arrow Multiple Line, Rectangle and Square, Rounded Rectangle and Square, Ellipse and Circle, Polygon and Curves. You can select any color for drawing lines and filling into objects.

All objects in LBDraw can be aligned to top, bottom, left or right. You can also move them forward or back in the third dimension.

Drawing tools for molecular biologists
In addition to above standard drawing tools, LBDraw provides tools specifically for molecular biologists: Double Strand DNA Structure, Needle, Virus, Bacteriaphage, Test Tube/Beaker and Flask.

You can fill with liquid (color) into Needle, Test Tube/Beaker and Flask. You can also regulate the levels of liquid in these containers.