brook at biology dot nmsu dot edu and his team at NMSU.
XYLEM is a package of tools designed to exploit the Unix environment to enable
the user to identify, extract and manipulate data from major databases such as
GenBank, EMBL and PIR.
brook at biology dot nmsu dot edu and his team at NMSU.
Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.
brook at biology dot nmsu dot edu and his team at NMSU.
GeneSplicer is a fast, flexible system for detecting splice sites in the
genomic DNA of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human,
Drosophila, and rice.
brook at biology dot nmsu dot edu and his team at NMSU.
FLUCTUATE fits the model which has a single population which has been
growing (or shrinking) according to an exponential growth law. It
estimates 4Nu and g, where N is the effective population size, u is
the neutral mutation rate per site, and g is the growth rate of the
population.
brook at biology dot nmsu dot edu and his team at NMSU.
COALESCE fits the model which has a single population of constant size, and
estimates 4Nu, where N is the effective population size and u is the neutral
mutation rate per site.
brook at biology dot nmsu dot edu and his team at NMSU.
SeWeR is SEquence Analysis using WEb Resources. It has web based Sequence
Analysis. SeWeR is an integrated portal to common web-based services in
bioinformatics.
brook at biology dot nmsu dot edu and his team at NMSU.
ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate
program for performing least squares fits of two protein structures. It
performs a very simple and basic function, but allows as much flexibility as
possible in performing this procedure. Thus one can specify subsets of atoms
to be considered, specify zones to be fitted by number, sequence, or by
sequence alignment.
brook at biology dot nmsu dot edu and his team at NMSU.
Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system.
brook at biology dot nmsu dot edu and his team at NMSU.
HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries. HMMER takes
multiple sequence alignement as input and builds statistical model
called "Hidden Markov Model" which can be used as a query into a
sequence database to find and/or align additional homologues of the
sequence family.
brook at biology dot nmsu dot edu and his team at NMSU.
GP is a set of small utilities written in ANSI C to manipulate
DNA sequences in a Unix fashion, fit for combining within shell
and cgi scripts.
Given a GCG multiple sequence alignment file (a GCG MSF file), which a
includes a sequence of known structure, the program pdbalign maps the
sequence variability onto the known structure. The central premise is
of course, that for a closely related family of proteins (sequence ID
> 40%) the 3-D structures will not be significantly different.pdbdist
calculates the distance from each atom in the pdb file to each atom in
the ligand and records the minimum in the temperature field for that
atom record.distalign reads the output from pdbdist and also the
original GCG MSF file and produces an MSF file annotated with a
measure of sequence variability and the distance of the residue at
that position (of the sequence of known structure) from the ligand.
brook at biology dot nmsu dot edu and his team at NMSU.
Given a GCG multiple sequence alignment file (a GCG MSF file), which a
includes a sequence of known structure, the program pdbalign maps the
sequence variability onto the known structure. The central premise is
of course, that for a closely related family of proteins (sequence ID
> 40%) the 3-D structures will not be significantly different.pdbdist
calculates the distance from each atom in the pdb file to each atom in
the ligand and records the minimum in the temperature field for that
atom record.distalign reads the output from pdbdist and also the
original GCG MSF file and produces an MSF file annotated with a
measure of sequence variability and the distance of the residue at
that position (of the sequence of known structure) from the ligand.
USE_GCC2 or USE_GCC3 where appropriate.
the functionality of the old gcc.buildlink2.mk has been rolled into
compiler.mk now, which is automatically used.
more changes to come later...
New features in chemtool 1.6
- universal import mode based on BABEL (both openbabel and babel supported)
- Formula weight calculator now handles all main group elements and the first
row of transition elements, and accepts greek phi as phenyl substituent.
- Movable hexagonal or square grid backdrop
- Improved SVG export, optional preview bitmaps in EPS export, optional EMF
export
- Cursor key support for pixel-precise drawing and moving
- The cleanup function now corrects bonds that deviate from ideal
horizontal or vertical orientation by a single pixel
- Color support (bonds and text can be red,green,blue,cyan,magenta or yellow).
- Default bond length now configurable, additional grid positions at two and
three times this length added
- Added a brief help text to accompany the 'About' window in the 'Help' menu.
- Added alternate text font (Times Roman)
- An attachment site can be marked before saving a molecule or fragment,
which act as reference point for adding this fragment to other molecules
(previously, this had to be the first atom in a file). Attachment sites are
marked in the preview window by a small x.
- Background color can now be chosen for screen display and EPS export, and
drawing whiteout boxes under labels is now an option ( off by default !).
- Text at 8,10,12,14,17,20 and 24pt can now coexist in a drawing.
- Increased allowed label length to 100.
- Improved rendering of dashed wedge and dotted lines
- Improved text kerning in xfig-based print and export.
- It is now possible to place an auto-incrementing counter at the cursor
position for numbering sites.
- Changed double bond drawing code to no longer switch sides depending
on drawing (or rotation) angle. (As a result of this, some older drawings
will need fixing)
- Rescaling a molecule now also scales its labels. Downscaling beyond
zero size (causing strange inversions) is no longer possible.
- Renamed the "Orbitals" template menu to "Symbols" and added "plus",
"minus" and a rearrangement arrow to it.
- Added two new bond types, a triple bond with all three lines equal,
and a quadruple bond.
Changes: This release introduces the new USDA Nutrient Database,
SR16, which has 6,661 foods and 125 nutrients, and includes an
automatic conversion feature so that NUT 8.x installations can
preserve existing meal records and have them interpreted with the
latest USDA database.
now and not NetBSD-*-arm32. Changes include one or more of:
- Change MACHINE_ARCH == arm32 to also match arm
- Where ONLY_FOR_PLATFORM includes NetBSD-*-arm32, add NetBSD-*-arm
- Where BROKEN or worked around for arm gcc bugs, set USE_GCC3
The last may shake out a few more broken packages the next bulk build.
Revision history for Bioperl core modules
0.7 Large number of changes, including refactoring of the
Object system, new parsers, new functionality and
all round better system. Highlights are:
o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
Bio::Root::IO for I/O and file/handle capabilities.
o Imported BPlite modules from Ian Korf for BLAST
parsing. This is considered the supported BLAST parser;
Bio::Tools::Blast.pm will eventually phase out due to lack of support.
o Improved Sequence Feature model. Added complete location
modelling (with fuzzy and compound locations). See
Bio::LocationI and the modules under Bio/Location. Added
support in Genbank/EMBL format parsing to completely parse
feature tables for complex locations.
o Moved special support for databanks etc to specialized modules under
Bio/Seq/. One of these supports very large sequences through
a temporary file as a backend.
o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
CDS retrieval and exon shuffling.
o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
DB/GDB (the latter has platform-specific limitations).
o New analysis parser framework for HT sequence annotation (see
Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
o New Alignment IO framework
o New Index modules (Swissprot)
o New modules for running Blast within perl
(Bio::Tools::Run::StandAloneBlast). Added modules for running
Multiple Sequence Alignment tools ClustalW and TCoffee
(Bio::Tools::Run::Alignment).
o New Cookbook-style tutorial (see bptutorial.pl). Improved
documentation across the package.
o Much improved cross platform support. Many known incompatibilities
have been fixed; however, NT and Mac do not work across the entire
setup (see PLATFORMS).
o Many bug fixes, code restructuring, etc. Overall stability and
maintainability benefit a lot.
o A total of 957 automatic tests
0.6.2
There are very few functionality changes but a large
number of software improvements/bug fixes across the package.
o The EMBL/GenBank parsing are improved.
o The Swissprot reading is improved. Swissprot writing
is disabled as it doesn't work at all. This needs to
wait for 0.7 release
o BLAST reports with no hits are correctly parsed.
o Several other bugs of the BLAST parser (regular expressions, ...)
fixed.
o Old syntax calls have been replaced with more modern syntax
o Modules that did not work at all, in particular the Sim4
set have been removed
o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
have improved compliance with interface specs and documentation
o Mailing list documentation updated throughout the distribution
o Most minor bug fixes have happened.
o The scripts in /examples now work and have the modern syntax
rather than the deprecated syntax
0.6.1 Sun April 2 2000
o Sequences can have Sequence Features attached to them
- The sequence features can be read from or written to
EMBL and GenBank style flat files
o Objects for Annotation, including References (but not
full medline abstracts), Database links and Comments are
provided
o A Species object to represent nodes on a taxonomy tree
is provided
o The ability to parse HMMER and Sim4 output has been added
o The Blast parsing has been improved, with better PSI-BLAST
support and better overall behaviour.
o Flat file indexed databases provide both random access
and sequential access to their component sequences.
o A CodonTable object has been written with all known
CodonTables accessible.
o A number of new lightweight analysis tools have been
added, such as molecular weight determination.
The 0.6 release also has improved software engineering
o The sequence objects have been rewritten, providing more
maintainable and easier to implement objects. These
objects are backwardly compatible with the 0.05.1 objects
o Many objects are defined in terms of interfaces and then
a Perl implementation has been provided. The interfaces
are found in the 'I' files (module names ending in 'I').
This means that it is possible to wrap C/CORBA/SQL access
as true "bioperl" objects, compatible with the rest of
bioperl.
o The SeqIO system has been overhauled to provide better
processing and perl-like automatic interpretation of <>
over arguments.
o Many more tests have been added (a total of 172 automatic
tests are now run before release).
0.05.1 Tue Jun 29 05:30:44 1999
- Central distribution now requires Perl 5.004. This was
done to get around 5.003-based problems in Bio/Index/*
and SimpleAlign.
- Various bug fixes in the Bio::Tools::Blast modules
including better exception handling and PSI-Blast
support. See Bio/Tools/Blast/CHANGES for more.
- Fixed the Parse mechanism in Seq.pm to use readseq.
Follow the instructions in README for how to install
it (basically, you have to edit Parse.pm).
- Improved documentation of Seq.pm, indicating where
objects are returned and where strings are returned.
- Fixed uninitialized warnings in Bio::Root::Object.pm
and Bio::Tools::SeqPattern.pm.
- Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
0.05 Sun Apr 25 01:14:11 1999
- Bio::Tools::Blast modules have less memory problems
and faster parsing. Webblast uses LWP and supports
more functionality. See Bio/Tools/Blast/CHANGES for more.
- The Bio::SeqIO system has been started, moving the
sequence reformatting code out of the sequence object
- The Bio::Index:: system has been started, providing
generic index capabilities and specifically works for
Fasta formatted databases and EMBL .dat formatted
databases
- The Bio::DB:: system started, providing access to
databases, both via flat file + index (see above) and
via http to NCBI
- The scripts/ directory, where industrial strength scripts
are put has been started.
- Many changes - a better distribution all round.
1.3a1 Fixed and restored XBM export. Added a (almost empty) template menu
(the beginnings of which were already hidden in 1.2a8). Fixed kerning
of mixed sub- and superscripts (as in SO_4^2^-). Changed allocation of
initial drawing area, calculate actual size before saving.
1.3a2 Added option menu for default bond type , added label support to
template function
1.3a3 Reduced preallocated drawing area to 'windowsize+100', as the increase
in 1.3a1 (which used window+1000) caused a massive slowdown at startup.
Freed unneeded pixmaps in the button setup code.
Fragment rotation code now stores the initial coordinates and uses them
as basis for the new positions - the previous, incremental calculation
was severely plagued by accumulation of errors.
1.3a4 Changed bond option menu to use small icons instead of longer and less
clear text labels. Removed check for 'cursor inside marked region' in
'Move' mode to allow smooth dragging. Started populating the O and N
heterocycle panels of the template menu. Fixed a duplicate bond in the
tcdd example, and removed those examples that have become templates.
1.3a5 Added shortcut for some labels - pressing c,n,o,s,p,r,i,h,d or b
inserts the corresponding centered element symbol at the last
drawing position, 'l','1','2','3' insert the left justified labels
'Cl','CH','CH_2','CH_3'. Fixed a GC leak in export_bitmap.
1.3a6 Moved the nucleoside examples to the template system. Made marker
position default to last drawing position, so that the 'Add' function
is now always active. Beginnings of internationalization (.mo file
for German locale added). Fixed naphthalene template, added dicyclo-
pentadiene. Changed Add_atom to automatically convert blanks in label
input to backslashes for storage. Prepared a few drawings for later
inclusion in the template system (camphor,pteridine,caffeine,glucose,
fructose,mannose,galactose,neuraminic acid, spiro[4.5]decane).
1.3a7 Template cleanup: porphine moved to heterocycle panel, spirodecane
added in its place. Glc,Fru,Man,Gal transfered to carbohydrate
templates, caffeine to heterocycles. Czech translation (by Radek
Liboska) added. Improved bounding box coordinates for xfig compound
object (used for sub/superscripted labels) Changed export functions
to remove the intermediate '.f2l' files. Changed orientation in xfig
header to Portrait. Adapted xfig (and xfig-based) export modes to
the new XFig default depth of 100. Changed depth of xfig text (labels)
to 90 and added filled white polygons at depth 95 to hide overlapping
line segments (experimental, used only for sub/superscripted text at
the moment). Reset default filename to 'unnamed' when the current
molecule is deleted.
1.3a8 Changed buttons mark/move/rotate/flip/delete/copy from text to icon
to reclaim space for the text entry box (icons created by Radek
Liboska). Added white polygon to clear area under normal text as well.
1.3a9 Added program icon. Added an interface for Radek Liboskas standalone
program CHT, which calculates sum formula and molecular weight from
a chemtool sketch. Corrected example drawing of brevetoxin.
1.3a10 Really reset mark flag when nothing was within the marker box.
Allow saving only the marked region (formula weight computation only).
Helper program CHT now parses those labels that are not in its
internal table of common substituents; exact mass is now returned
automatically.Added status line with message history.
1.3a11 Internationalization support made optional (define DISABLE_NLS in
the Imakefile if you do not want it) to allow compiling on systems
without GNU-style locale support again.
Improved ring size and position in the benzene and cyclopentadiene
templates (Michael Banck). Reset all marks before loading a template.
If the template menu is already open, pressing the Template button now
brings it to the front. Added templates (inden,biphenyl), removed the
ugly question mark placeholders.
Changed handling of windowmanager events, so that using the window
decorations' CLOSE button brings up the Yes/No dialog while the
chemtool window is still alive.
Changes in helper program CHT (cht011a): now recognizes Ac in complex
substituents; correctly handles aromatic 'ring' in formula input;
checks input file for identifier "Chemtool"; reads number of bonds
from "bonds" line (to handle label-only files gracefully); exits on
unattached labels instead of silently miscalculating formula and
mass. Subsequently updated to Radek Liboskas current version 0.19,
which already includes equivalent changes. Added list of abbreviations
supported by cht.
1.3a12 Reset all marks before 'adding' a sketch. Adding a label on top of an
existing one now replaces the old label as it should. Added a function
for rescaling objects (useful for drawing reagents above the reaction
arrow - but labels are not rescaled yet). Added linetype 13, a single
bond with opaque background (for crossing bonds - see the bicyclooctane
template). Updated the German translation.
This - plus or minus some templates - is my release candidate for 1.3.
1.3a13 Dropped the internal icon, as it was only causing trouble, especially
with KDE. Most window managers allow specification of an external icon
anyway (added chemtool.xpm for this purpose). Moved 'delete fragment'
button to the end of the button row. Updated Czech translation by
Radek Liboska. Added linetype 13 to the helper program CHT, made it
accept any Chemtool 1.x file, not only version 1.2. Updated the
'documentation', i.e. the README file, split out an INSTALL file. Set
version number in chemtool files to 1.3. Fixed bug that left a newly
'added' structure active but unable to move. Rewrote positioning
logic for subscripts and right-justified text in export modes again.
Changed screen display of molecule from 'fixed' fonts to helvetica
as used in the export modes - previously, labels that appeared fine
on screen could overlap in the final (postscript) output. Fixed
'mannose' template that showed exactly this. Added formatting option
'|' for slanted characters (as in iPr,tBu).
1.3a14 Fixed label shortcuts for CH_2 and CH_3 that could crash chemtool
(buffer overrun). Fixed scaling in export function , which had been
applied to labels only. Improved label size at smallest scale. Added
correction factor for sub/superscript after certain characters (the joys
of proportionally-spaced fonts :-( ). Handled reopening of template menu
after a close via the window manager. Updated 'About' menu (mention Radek
Liboska as developer, add the tu-darmstadt webpage).
1.3a15 Changed canvas bitmap allocation to avoid uncovering garbled portions
when the sliders are used. Fixed fragment deletion code (deletion of
the marked fragment and redisplay of the modified drawing are now
performed immediately). This hopefully fixes the crashes some people
have been seeing with this function.
1.3 Added Check for no (or no selected) atoms before trying to delete a
fragment, fixed bug that could deletion of a fragment to fail.
Changed functions for horizontal and vertical flip to transform the
atom(s) directly bonded to the marked fragment as well. Added current
filename (if any) to window title. Use xfig's own arrow type in export
of regular arrows (Michael Banck).
Some code cleanup: removed dead code, fixed unnecessary parameter
passing between functions, tidied formatting with GNU indent. Removed
Imakefile and provided regular Makefile (the build process relies on
gtk-config, not xmkmf, since 1.2), added install targets for the
localization files and manpage. Updated cht to version 1.3.
ones to do, and each compiled and installed/de-installed apparently
correctly.
As a side effect of the dynamic PLIST, we no longer need to have separate
-static and -shared PLISTs. It's now easier than ever to make a perl5
package for NetBSD :)
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images.
Submitted by Marc Bauoin <babafou@babafou.eu.org> in pkg/8199, slightly
enhanced.
for DNA or proteins. This is a merge of the packages submitted in PRs
pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor
modifications), thanks!
