CHANGELOG, 12 October 2003
add -X option to glimmer2, to allow orfs extending off ends of
sequence to be scored. Also fix bug affecting -p and -o options
when user chose zero overlap.
* The FASTA format has been added to the list of alignment output
options.
* It is now possible to save the residue ranges (appended after the
sequence names) when saving a specified range of the alignment.
* The efficiency of the neighour-joining algorithm has been improved.
This work was done by Tadashi Koike at the Center for Information
Biology and DNA Data Bank of Japan and FUJITSU Limited.
Some example speedups are given below : (timings on a SPARC64 CPU)
No. of sequences original NJ new NJ
200 0' 12" 0.1"
500 9' 19" 1.4"
1000 XXXX 0' 31"
* ClustalW now returns error codes for some common errors when exiting.
This may be useful for people who run clustalw automatically from within
a script.
Error codes are:
1 bad command line option
2 cannot open sequence file
3 wrong format in sequence file
4 sequence file contains only 1 sequence (for multiple
alignments)
* Alignments can now be saved in Nexus format, for compatibility with
PAUP, MacClade etc. For a description of the Nexus format, see:
Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997.
NEXUS: an extensible file format for systematic information.
Systematic Biology 46:590-621.
* Phylogenetic trees can also be saved in nexus format.
* A ClustalW icon has been designed for MAC and PC systems.
10.1:
This release adds a fix for zero values that display as no data.
10.0:
This release updates the USDA Nutrient Database to version SR17, and allows
current NUT installations to have their existing meal records reinterpreted
with the new database.
9.20:
This release optimizes the new code of the last release, the focus of which
was distinguishing no data from zero in the USDA database.
9.19:
The program now distinguishes between zero values and no data in the USDA
database, and uses this information to produce a new screen that lists foods
high in some nutrient while minimizing some other nutrient.
9.18:
This release contains revisions to the polyunsaturated fatty acid reference
values and how they scale up as fats increase and carbs decrease.
9.17:
This release provides what may be more reasonable or optimal default settings
for fat percentages when the user sets the program for low carb.
9.16:
This release contains bugfixes for a segmentation fault which occurred when
entering a control-D and a monounsaturated fat reference value that was too
high.
9.15:
This release makes serving sizes more consistent among food groups. It adds
functions to change the default serving size, and to sort foods by nutrients
per serving.
9.14:
This release adds support for an optional database subdirectory, allowing the
user to easily maintain multiple databases, for multiple family members, for
instance. It also adds display of non-fiber carbohydrate grams ("net carbs")
on the main analysis screen.
9.13:
The program now allows commercial foods that have a nutrition label and an
ordered ingredients statement to be added to the food database. An
approximation to a food's recipe is found that best fits the criteria and the
recipe is analyzed to provide information about the additional nutrients not
stated on the nutrition label.
9.12:
[unknown]
Update distinfo for new archive. Only minor bug fixes, no version change.
For a detailed diff, see:
ftp://ftp.netbsd.org/pub/NetBSD/misc/ben/profit-2004-08-14.txt
This addresses PR#26656 from Georg Schwarz.
New in 9.11:
Because the program uses the approximation of 4 calories per gram
for carbohydrate and protein to analyze meals according to the
"Daily Value" -- although real food has various values for calories
per gram -- the program now refigures fat percentage values at each
analysis so that when calories, carbs, and protein are each at
exactly 100%, fat will be also.
New in 9.10:
This release fixes a buffer overflow in the food selection function
which caused the program to not find certain foods even though they
existed in the database.
New in 9.9:
A bug has been fixed in which during food selection, the program
lost the value of the food name key. Also, some of the program's
reference values for the essential fatty acids have been modified.
New in 9.8:
The program now defaults to either grams or ounces, depending on
the weight unit the user enters to specify servings. A bug in
handling customary meal names that are too long has been fixed.
New in 9.7:
The program computes essential fatty acid reference values based
on the user's diet. Prior releases aimed toward a particular balance
of Omega-6 and Omega-3. This release allows the user to specify
the balance between Omega-6 and Omega-3 without having to determine
the amount of the individual fatty acids.
New in 9.6:
The program is now capable of understanding food names in simple
English, such as "fried chicken" and "mashed potatoes." This is
accomplished by including the list of abbreviations the USDA uses
and by successively searching for each tokenized term, whatever
the order in the USDA name.
9.5:
The last release introduced a bug when adding customary meals to
regular meals. The program now adds the foods without the additional
prompt screen.
9.4:
This release changes the method of searching for foods to a substring
search. The narrowing-down of food categories to a unique food is
the same as in prior releases.
This release fixes a bug in the graphs where the "Daily Value" was
such a small percentage of the values graphed that the DV line
indicator exceeded the graph width.
gcc3. While here, update to version 2.12 (previous version was erraneously
named 2.1, when it should have been 2.10) which is the only distfile
available on the ftp site.
Changelog seems to say:
- Fix bug on long-orfs.cc to avoid occasional array out-of-bounds
error (detected on Mac OS X).
9.2:
The upper limit of the polyunsaturated reference value for linoleic
acid has been reduced to 4% of calories, while that for alpha
linolenic acid has been raised to 2%. An internal constant for the
percentage of total fat that is fatty acids has been replaced by
a function that figures it for each analysis.
9.1:
The program is no longer limited to three meals a day, and can now
be set for 1 to 19 meals per day. A list of the meals not yet
recorded for a selected day is displayed as a mnemonic during the
"Record Meals" function.
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.
