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.
