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DNA Strider A bit dated but still great full featured sequence manipulation application for the mac. Unfortunately Strider will not run on recent Macs, as it requires a 'Classic' environment. Will work great on older machines; Linux Software for Molecular Biology and Bioinformatics. EScribe Suite is a collection of software for configuring, monitoring, and modifying the operation of your DNA device. It installs on a Windows or Mac computer and connects to your DNA device using the USB port. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner also import files saved in the Vector NTI, MacVector, ApE, DNAstar, pDRAW32 and GenBank formats. Import from VectorNTI multi-file format is also supported. Powerful graphical display tools and simple interfaces.
DNA Strider installation package is prepared to be downloaded from our fast download servers. It is checked for possible viruses and is proven to be 100% clean and safe. Various leading antiviruses have been used to test DNA Strider, if it contains any viruses. No infections have been found and downloading DNA Strider is completelly problem. Mac upgraded to OSX, Lepard which do not support os9 anymore. This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function. This program is still in early step of development, I release it now only because it can read out the old DNA Strider file correctly so that people can copy and paste to.
This is the homepage for Xdna2, a set of tools to convert biological sequence data from and to the binary file format used by the popular MacOS X program “DNA Strider”.
Xdna2 is distributed under the terms of the GNU General Public License.
This project is no longer under active development. It is replaced by a new project aiming to bring support for the DNA Strider format (and some other formats as well) to the SeqIO framework of Biopython.
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Usage
Dna Strider Mac Download Software
Xdna2 provides two programs to convert DNA Strider “.xdna” files from the command line. The xdna2 program converts a DNA Strider file to a FASTA or GenBank file; the 2xdna does the opposite, it converts a FASTA file to a DNA Strider file.
The DNA Strider binary format
As far as I can tell from the “.xdna” files that I have seen, the DNA Strider binary format is organized in three or four sections:
- a “header” containing informations such as the length and the type of the sequence;
- the sequence itself;
- a “comment”, a free-form text associated to the sequence.
- optionally, an “annotations” section.
The header has a fixed size of 112 bytes. See the src/xdna.h file and the
xdna_header_t
C structure for details. Important informations include: the sequence type (DNA, RNA, protein—byte 2); the sequence topology (linear or circular—byte 3); the length of the sequence (bytes 29–32); and the length of the comment (bytes 97–100).The sequence and the comment are plain text data. The sequence starts immediately after the header (byte 113); the comment starts immediately after the sequence (byte 113 + length of sequence).
Some .xdna files, such as those generated by Serial Cloner, contains an additional annotation section. This section starts by four fields describing the optional right and left overhangs (thanks to Cory Li, from the Benchling project, for details about the meaning of those fields). The next byte stores the count of annotation, and the annotations themselves are described in the remaining of the file.
Each annotation contains six fields; each field is a Pascal string beginning with one byte indicating the length of string, followed by the string itself. The fields are:
![Dna Dna](/uploads/1/2/6/6/126667804/408985581.jpg)
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- the annotation’s name;
- a comment about the annotation;
- the annotation’s type (CDS, promoter, rep_origin, and so on);
- the start position;
- the end position;
- an unknown field, containing three dot-separated numbers (I strongly suspect this is a RGB triplet indicating the color to use for displaying the annotation).
In addition, there are four bytes between the fifth and sixth field, three of them being boolean flags indicating the DNA strand, whether the annotation should be displayed, and whether it should be displayed with an arrow.
The table below summarizes the structure of a DNA Strider file.
Contents | Type | Size in bytes | Remarks |
Header section | |||
---|---|---|---|
version | integer | 1 | always zero? |
sequence type | integer | 1 | 1 = DNA, 2 = degenerate DNA, 3 = RNA, 4 = protein |
topology | integer | 1 | 0 = linear, 1 = circular |
padding | 25 | ||
sequence length | integer | 4 | big endian |
padding | 64 | ||
comment length | integer | 4 | big endian |
padding | 12 | ||
Sequence section | |||
sequence | ASCII chars | sequence length | |
Comment section | |||
comment | ASCII chars | comment length | |
Annotations section (optional) | |||
unknown byte | 1 | ||
ROH length | Pascal string | 1–256 | 0 = no overhang, < 0 = 3’ overhang, > 0 = 5’ overhang |
right overhang | ASCII chars | |ROH length| | |
LOH length | Pascal string | 1–256 | 0 = no overhang, < 0 = 3’ overhang, > 0 = 5’ overhang |
left overhang | ASCII chars | |LOH length| | |
annotations count | integer | 1 | |
Annotation subsection (one for eachannotation) | |||
feature name | Pascal string | 1–256 | |
feature description | Pascal string | 1–256 | |
feature type | Pascal string | 1–256 | |
start position | Pascal string | 1–256 | |
end position | Pascal string | 1–256 | |
strand flag | boolean | 1 | 0 = reverse, 1 = forward |
show flag | boolean | 1 | 0 = don’t show the feature on map, 1 = show |
unknown byte | 1 | ||
arrow flag | boolean | 1 | 0 = no arrow, 1 = arrow |
extra field | Pascal string | 1–256 |
Download
Download the last release tarball:
Dna Strider For Pc
xdna2-0.2.4.tar.gz (application/x-gzip, 197K, signature)