DNAMAN使用说明

DNAMAN for Windows DNAMAN uses advanced features of Microsoft Windows and offers versatile visual tools for sequence analysis. Sequence Manipulation 页码，1/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 can 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. You can directly access the Internet with DNAMAN through the Netscape browser. When you insert the browser into a document of the DNAMAN word processor, you can directly exchange information between your documents and the Internet. 页码，2/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 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. 页码，3/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m BLAST documents/Internet access 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 Examples: Sequence Search 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 can also provide multiple query sequences for searching. 页码，4/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m DNAMAN instantly reports the searching results in graphics. Colors and arrowheads indicate different sequence groups and sites. You can magnify any region of the DNA fragment and display the regional sequence of by selection. The versatility of query sequences and graphical presentations make the search function useful in many other areas, such as presenting restriction sites, elements and gene structures. 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 页码，5/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m You can search for open reading frames from six reading frames of a DNA sequence. The searching result is shown in a text table. DNAMAN can also display the result in a graphic window. Search for repeat sequences You can 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 can 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 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. 页码，6/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 tools to design a cloning strategy and performs evaluation analyses on target sequences. This feature could improve the efficiency of your cloning work in 页码，7/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m laboratory. DNAMAN mimics basic steps of the actual cloning process: l Restriction analysis on the original vector and insert sequences l Selection of vector and insert fragments from restriction pattern l Verification of the end compatibility of DNA fragments l Modification of fragment ends if necessary l Insertion of linkers if necessary l 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 页码，8/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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: l Graphic window provides an overview of the assembly construction. You can edit this graphical presentation to produce high quality diagrams for publications. l Name list window contains all assembled sequence names. You can change the sequence order by moving the sequence names in this window. l 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 With DNAMAN, you can compare two DNA sequences or two protein sequences in a dot matrix plot. There are two methods for comparison. Method 1 uses a fast algorithm and is suitable for long sequences. Method 2 performs progressive comparison to reduce the background of low homology regions. The two methods yield different speed and accuracy in analysis. DNAMAN displays the actual sequences and their alignment on any selected region in a sequence 页码，9/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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. 页码，10/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m Multiple Sequence Alignment Multiple sequence alignment methods Fast alignment DNAMAN uses Wilbur and Lipman algorithm for fast alignment. You can quickly align a large number of DNA or protein sequences. This algorithm is able to produce an accurate alignment if sequence divergence is low. Optimal alignment Feng-Doolittle and Thompson method (CLUSTAL) is used for optimal sequence alignment. You can input individual sequences and/or multiple alignment profiles. There are three types of alignment: l Full alignment to completely align all sequences. l Profile alignment to align two multiple alignment profiles without disturbing the original alignments. l New sequence on profile to align a new sequence with an existing multiple alignment profile. You can optimize multiple alignment by selecting alignment criteria in the easy panel. 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. 页码，11/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m You can modify the appearance of multiple alignment sequences: l displaying identical residues in colors or blocks l displaying consensus sequence l changing text font Multiple alignment input and output You can directly input sequences or multiple alignment profiles for alignment from the following sources: l GenBank, l EMBL/Swiss Prot, l GCG/MSF, l CUSTAL, l FASTA, l NBRF/PIR l GDE The multiple alignment editor can output an alignment in different formats: 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. 页码，12/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 页码，13/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m developed by King and Sternberg. Primer Analysis 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. l 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. l You can carry out a restriction analysis on the primers in order to select those with or without restriction site(s). l 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 hybridization. You can also have the Tm information on the hybridization of 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. l Self-complementary DNAMAN searches for the most possible self-complementary configuration of primers with the lowest free energy. l Complementarity with target DNA DNAMAN searches for the complementary sequences between the primer and both stands of target DNA. l Two primer complementarity 页码，14/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 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 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 can select any genetic code table for translation and protein 页码，15/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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. 页码，16/33DNAMAN 2009-2-24mhtml:file://C:\Documents%20and%20Settings\bbioo\Local%20Settings\T... 生 物 秀 -专 心 做 生 物 ww w. bb ioo .co m 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 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. l Any oligo database is expandable and all records are editable. l You can provide information for each record in seven fields: name, source, memo, length, GC content, melting temperature and sequence. l The name, source, memo, length can be used as sorting keys. l 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 databas