生物化学分子生物学软件下载区-DNATools

DNATools is intended to assist you in routine manipulations of DNA sequences retrieved from data bases or generated by yourself by automatic or manual sequencing. The program has no ambition of competing with more complex - and more expensive - analysis programs such as the Wiscounsin GCG package, LaserGene, DNAsis, etc. They can all carry out about the same operaions as DNATools, faster and with longer sequences.
The design of DNATools has been focussed on creating a user friendly, robust application adapted for fast and convenient retrieval, storing and analysis of sequences and sequence related information such as results of data base searches.
DNATools is tolerant and lets you open almost any text document as a sequence. If the progeam fails to identify the format of the sequence (by looking for features characterizing the most common sequence formats) program displays the text document letting you edit the text to yield a proper protein or DNA sequence - which can then be loaded into the program. If your sequence is in DNATools format (a DNA sequence or an oligo nucleotide) it is loaded without comments and the program mode is adjusted to accept the loaded type of data (protein and DNA sequences and oligo nucleotide primers).
You can load several thousand sequences or primers into a single project and analyse the sequences and/or their headers across the entire project.
A key feature of the program is the extended use of the text header attached to each sequence or primer. The common problem of identifying sequences by their file name is avoided by the option of viewing sequences by user-defined header lines.
Searching data bases usually generates piles of paper. With DNATools you can paste relevant search data into the header or your sequence instead. Each text header can hold several megabytes of data. SAGE (serial analysis of gene expression) data, information on overlapping sequences as well as northern blot data can conveiningly be incorporated into the separate data section of the header. The data header includes a special form for entering hybridization data for each sequence of the project. The two separate headers associated with each sequence file can be searched across the entire project.
Major parts of the program were developed during an EST (expressed sequence tags) sequencing project and therefore has a number of functions especially designed to facilitate operations involving many small sequences. Although the program does not create a true database to store your sequences, it behaves somewhat like a database program by enabeling you to search and compare several thousand sequences simultaneously.
To avoid loss of data - and of your work - DNATools includes several options for resqueing lost data: A 5-level undo/redo function, a restore function which retrieves the original sequence, a safety backup option when loading new files into a project and a timed backup function where a complete backup or your work is created and saved at selected intervals.

Imagine for example that you have completed a sequence run generating 36, 64 or 96 sequences named automatically by the sequencer: seq1, seq2, seq3 ... seq36 - or lane1, lane 2, lane3 ... lane 96. With DNATools you simply load all sequences into the program and use one of the three options for changing file names.
Maybe you want to make sure that the primers you just created actually matches the sequence from which they were derived. Just combine all the primer sequences in your project into a search data file and use this to search the mother sequence(s). If you want to find out if any of the primers you already have in you freezer match a particular sequence, simply load all your primers into a project and convert them to a search data file and carry out the search in the same way as you would do with a restriction enzyme file.
With DNATools you can easily keep track of a large number (many hundreds) of primers. Just keep all your primer files in the same directory and remember to enter a descriptive first or second line in the file header when you create the primer. If you want to find a particular primer simply load all primer files into a new project and list the files by first or second line of the header.
If you need more workspace just open one or more extra instances of DNATools, one for the sequence, a second to create primers, a third to display a data base sequence etc. Each instance gets its own ini file so you don't have to enter project title, source and target directory paths, font size and other settings each time.
Translation of complete sequences or extracts as well as searches for restriction sites are easily performed, the former being especially convienient when you make data base searches on internet servers. If a search at the DNA level fails, then just translate the sequence in one of six frames and repeat the search at the protein level. You can easily identify the longest contiguous amino acid sequence with the 'largest ORF in six frames' or 'largest fragment in six frames' functions. The basic properties (Mw, amino acid composition, pI, etc.) of the protein can be viewed on the amino acid form.
Screening libraries with degenerate primers is an efficient way of isolating new genes. The construction of degenerate primers is greatly facilitated by the options for selecting the degeneration level during back translation of peptide sequences. Creating species specific codon usage tables is another function which assists you in designing degenerate PCR primers.
A special orderform for electronic ordering is incorporated into DNATools facilitating ordering primers by e-mail. This also includes the option of encoding your order file before shipping it. Obviously this requires that the supplier has access to DNATools in order to decode the order.
When you have realised the scope of the program and accepted that you cannot do a multi-sequence alignment or a 500-sequence merge, I hope you will enjoy using DNATools and that you will find it helpful in your daily fight with DNA sequences and primers. Please feel free to report any bugs you may encounter in the program as well as suggestions for new functions. I have invested a great deal of effort in debugging and error trapping - being fully aware of the frustration one experiences when hours of work is lost because the program decides to quit without warning. However, a few bugs may have escaped my attention.
DNATools is a 32 bit application and runs under Windows95/98 and Windows NT 4.0. It is recommended that the PC is at least 100 MHz and has more than 32 Mb of RAM.
You can use DNATools for a period of 3 months free of charge. The cost of a non-commercial, single user licence is $100.

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