DegenPrimer

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2.8 release from the trunk series released

Release information
Release notes:

  * New robust termination mechanism.

  * Calculation progress display was added.

  * Naming of configuration files and results now depends on analysis parameters. No more overwriting of previous results.

  * Automatic logging of all output to a file.

  * PBS support (see pbs-utils package on PyPi).

Changelog:

  * New robust termination mechanism.

  * Calculation progress display was added.

  * Naming of configuration files and results now depends on analysis parameters. No more overwriting of previous results.

  * Automatic logging of all output to a file.

  * PBS support (see pbs-utils package on PyPi).

File Description Downloads
download icon degen-primer_2.8-rc2.orig.tar.gz (md5, sig) Version 2.8-rc2 86
last downloaded 18 weeks ago
Total downloads: 86

2.1 release from the trunk series released

Release information
Release notes:

* ipcress from exonerate package is no longer used. Search for primers' annealing sites is implemented inside degen_primer using fft-based algorithm which depends only on scipy. This algorithm is considerably faster and less memory demanding.
* Some bugfixes and optimisations were made, especially in PCR simulation which now wokrs several times faster as well.
* More steps in the analysis pipeline are parallelized to take advantage of multicore systems.

File Description Downloads
download icon degen-primer_2.1-rc1.orig.tar.gz (md5, sig) Version 2.1-rc1 33
last downloaded 41 weeks ago
Total downloads: 33

2.0 release from the trunk series released

Release information
Release notes:

iPCR rewritten from scratch. It is now a full simulation of a PCR reaction.
Also many improvements in speed, interface and report formatting.
Bugfixes.

The work is still in progres...

File Description Downloads
download icon degen-primer_2.0-rc5.orig.tar.gz (md5, sig) Version 2.0-rc5 14
last downloaded 17 weeks ago
Total downloads: 14

1.6 release from the trunk series released

Release information
Release notes:

Bufgixes.
Value constraints check of input data.
Improved Tm prediction with primer concentrations.
DMSO correction of predicted Tm.

Changelog:

Bufgixes.
Value constraints check of input data.
Improved Tm prediction with primer concentrations.
DMSO correction of predicted Tm.

File Description Downloads
download icon degen-primer_1.6.orig.tar.gz (md5, sig) Version 1.6 16
last downloaded 17 weeks ago
Total downloads: 16

1.5 release from the trunk series released

Release information
Release notes:

Saved BLAST-results are now reparced with current settings by default if --do-blast is not set.

Changelog:

Saved BLAST-results are now reparced with current settings by default if --do-blast is not set.

File Description Downloads
download icon degen-primer_1.5.orig.tar.gz (md5, sig) Version 1.5 13
last downloaded 17 weeks ago
Total downloads: 13

1.4 release from the trunk series released

File Description Downloads
download icon degen-primer_1.4.orig.tar.gz (md5, sig) Version 1.4 12
last downloaded 41 weeks ago
Total downloads: 12

1.3 release from the trunk series released

Release information
Changelog:

Primer may be provided not only as a raw sequence but as a fasta or genbank file.

File Description Downloads
download icon degen-primer_1.3.orig.tar.gz (md5, sig) Version 1.3 12
last downloaded 17 weeks ago
Total downloads: 12

1.2 release from the trunk series released

Release information
Changelog:

Fixed redundant BLAST query composition. => Much faster searches, less repeating results.
New BLAST results filtration by iPCR parameters.
New iPCR with BLAST results!
Minor bugfixes.

File Description Downloads
download icon degen-primer_1.2.orig.tar.gz (md5, sig) Version 1.2 11
last downloaded 41 weeks ago
Total downloads: 11