MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'alignment'. Sat, 03 Sep 2011 02:23:04 +0100 http://www.medworm.com/index.php?rid=5159301&cid=t_167197_113_f&fid=35744&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fe-CareManagement%2F%7E3%2F6e23a3ZIUP8%2F by Jaan Sidorov MD, MHSA, FACP and Vince Kuraitis JD, MBA Physicians face great uncertainty. According to a survey conducted by The Physicians Foundation, the great majority of physicians (89%) believe the traditional model of independent private practice is either “on shaky ground” or “is a dinosaur soon to go extinct.” In the face of this uncertainty, many physicians are jumping to a conclusion that “I have to sell my practice to the hospital.” In this post of our series on The 100 Year Shift, we will examine physician practice.  We’ll show that the economic and clinical environment  is changing rapidly and that selling to the hospital is one option. However, it is not the only option. (more…) Article Series - The 100 Year Shift? Strategic ... e-CareManagement blogs http://www.medworm.com/rss/comments.php?id=5159301 Mon, 22 Aug 2011 15:26:12 +0100 5159301 http://www.medworm.com/index.php?rid=5008373&cid=t_167197_113_f&fid=35744&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fe-CareManagement%2F%7E3%2FIJUiE1aXZqA%2F by Vince Kuraitis JD, MBA and Jaan Sidorov MD, MHSA, FACP Gazing at the horizon, we foresee the potential for a tectonic realignment among physicians, hospitals and payers. Here’s a quick visual representation: This essay is the first of a seven part series. In this first post we will capsulize our vision of this potential 100 Year Shift, answer initial FAQs, and lay out the structure for the rest of the series. The Lynchpin — Changing Economic Incentives In the past, physicians and hospitals have benefited from mutually supportive economic interests. (more…) Article Series - The 100 Year Shift? Strategic Realignment among Physicians, Hospitals and PayersThe 100 Year Shift? Introduction and OverviewPayment Transformation: From Volume to Value Next in series Tags: 100 Yea... e-CareManagement blogs http://www.medworm.com/rss/comments.php?id=5008373 Tue, 05 Jul 2011 17:26:33 +0100 5008373 http://www.medworm.com/index.php?rid=4975988&cid=t_167197_113_f&fid=35744&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fe-CareManagement%2F%7E3%2FKNUpsAvSVXc%2F A study released last week by the Massachusetts Attorney General contains surprising data to challenge two commonly held ACO (accountable care organization) ”Field of Dreams” assumptions. These assumptions relate to patient ”leakage” — out-of-network patient care and referrals. 1) Hospital administrators assume that tighter physician-hospital integration (e.g., through employment of physicians) will result in ”captive referrals” by physicians back to the mother-ship hospital. 2) Medicare administrators are assuming that Medicare Shared Savings ACOs will be able to coordinate patient care even without limitations on patients’ choice to go to providers outside of the ACO provider network. Here’s the data that challenges the validity of ... e-CareManagement blogs http://www.medworm.com/rss/comments.php?id=4975988 Mon, 27 Jun 2011 18:21:41 +0100 4975988 http://www.medworm.com/index.php?rid=4934162&cid=t_167197_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fwhat-to-do-about-runners-knee-patellofemoral-pain-syndrome%2F2011.06.15 My left knee hurts. When I put weight on it with my leg bent, like when I get out of the car, I feel a dull pain in my knee. My doctor and physical therapist have given me a diagnosis of patellofemoral pain syndrome, also known as “runner’s knee” or patellar knee-tracking syndrome. Simply put, my kneecap doesn’t run smoothly up and down its track—a groove called the trochlea. Anyone can get patellofemoral pain syndrome, but for some reason it is more common in women than men—especially in mid-life women who’ve been running for many years. The problem, say researchers who just published a study in the journal Gait and Posture, is that lots of “mature” women develop alignment problems with their knees. The researchers compared younger female runners to older female runners ... Better Health blogs http://www.medworm.com/rss/comments.php?id=4934162 Wed, 15 Jun 2011 21:00:49 +0100 4934162 http://www.medworm.com/index.php?rid=4117881&cid=t_167197_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2Fp2NN3Sk-Aro%2F This week’s addition to the virology toolbox was written by Chris Upton (Disclaimer: BBB was developed in the Upton lab, so this is a biased review.) This will be a multi-part posting describing the key features of BBB. Base-By-Base (BBB) is a Java (platform independent) multiple sequence alignment (MSA) editor. Development was begun many years ago to provide a virologist-friendly tool to work with MSAs of proteins, gene sequences and also genome sequences (up to about 500 kb). Over the years we have added many unique features, as they have been needed by our own research with a variety of virus genomes; development has been driven by the users – who spend a lot of their day looking at a variety of MSAs! BBB is available here. The program is Open Source and freely available to all acad... virology blog blogs http://www.medworm.com/rss/comments.php?id=4117881 Tue, 26 Oct 2010 21:55:02 +0100 4117881 http://www.medworm.com/index.php?rid=4085962&cid=t_167197_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FNqu0iOoEXbw%2F This week’s addition to the virology toolbox was written by Chris Upton The Jalview package: a multiple alignment editor. This software is primarily aimed at the alignment of protein sequences. Some of the key features are: It allows you to edit the alignment It has functions to display associated protein structures It can connect to software to predict protein secondary structure It’s under active development Jalview has great documentation and tutorials More: Overview, Documentation Tips: Although you can install Jalview on your computer very easily, using the Start with Java Web Start button is even easier and ensures you always have the latest version of the software. There is also an Applet version of Jalview that is intended to be an alignment viewer – it doesn’t have ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4085962 Wed, 20 Oct 2010 19:19:07 +0100 4085962 http://www.medworm.com/index.php?rid=4073526&cid=t_167197_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FvHqbPksYzRM%2F This week’s addition to the virology toolbox was written by Chris Upton Generating multiple sequence alignments (MSA) is one of the most commonly used bioinformatics techniques. The “sequences” to be compared can be DNA (promoters, genes, genomes) or proteins. Note that the length and number of sequences to be aligned has an impact on the methods (algorithms) that can be used; what is suitable for aligning 20 proteins probably won’t work for alignment of 5 poxvirus genomes (200 kb each). Some useful links: Wikipedia: multiple sequence alignment Wikipedia: sequence alignment Wikipedia: list of sequence alignment software Protein Multiple Sequence Alignment: Book chapter by Chuong B. Do and Kazutaka Katoh Sequence alignment: Lecture notes by Per Kraulis Another list of tools So yo... virology blog blogs http://www.medworm.com/rss/comments.php?id=4073526 Fri, 15 Oct 2010 16:24:12 +0100 4073526 http://www.medworm.com/index.php?rid=3231108&cid=t_167197_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F02%2Fmicrobial-phylogenetics-methods.html The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In a... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3231108 Tue, 02 Feb 2010 14:25:00 +0100 3231108 http://www.medworm.com/index.php?rid=3030034&cid=t_167197_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fv5mHDKYmEjw%2F Image via Wikipedia Yes, DIALIGN-TX has all the problems with scientific software. All of them in 1.8 Mb of data, and I’m being kind. Let me explain that. I have this small project, and DIALIGN-TX is one of the programs I want to check. I compiled fine, or so I think: it runs ok on the Mac, shows me the parameters to run it, in a large list of options. Most of these options have a “DEFAULT” value, which means they are not needed to run the program. And there’s an usage example Usage: dialign-t [OPTIONS] [] (notice the error on the usage, I just copied and pasted) I tried every possible combination, with and without options, setting and not setting them, with different input files, no one worked. Then I decided to read the documentation. No true. First I decided ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3030034 Thu, 26 Nov 2009 14:21:06 +0100 3030034 http://www.medworm.com/index.php?rid=2902912&cid=t_167197_132_f&fid=35001&url=http%3A%2F%2Farchive.nodalpoint.org%2F2009%2F04%2F23%2Funder_maffts_hood Hello I am trying to learn what exactly MAFFT does to align sequences, but i am currently having a hard time to understand it. I have read its papers and references. Anyone knows of some kind of tutorial or review for it? I am researching the FFT-NS-i and E-INS-i algorithms. Currently, i am trying to understand what are the 6-tuples parameters. I guess the 6-tuples are the weight, volume and charge, compared in pairs of sequences. Is that right? Thanks in advance EDIT: Just in case someone is interested: read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=2902912 Fri, 24 Apr 2009 03:29:54 +0100 2902912 http://www.medworm.com/index.php?rid=2902919&cid=t_167197_132_f&fid=35001&url=http%3A%2F%2Farchive.nodalpoint.org%2F2008%2F07%2F25%2Fhow_history_affects_pattern_matching_inside_the_genome In a recent Science magazine article, Löytynoja-Goldman showed that all current Multiple Sequence Alignment algorithms – the bread-and-butter algorithm for biologists studying similarities in genes across different species – completely fail to detect independent insertions in the alignment of sequences, and thus, erroneously mismatches regions of evolutionary volatility. In their improved MSA algorithm, PRANK, they use history itself to improve the performance of this basic algorithm. [more...] (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=2902919 Fri, 25 Jul 2008 22:28:33 +0100 2902919 http://www.medworm.com/index.php?rid=1331519&cid=t_167197_132_f&fid=35624&url=http%3A%2F%2Fsuicyte.wordpress.com%2F2008%2F03%2F27%2Fstrange-paper-i%2F This week, I found two strange but interesting papers, one from the area of bioinformatics, the other from gene silencing. The unifying topic is that in both published works something went wrong, but the results were nevertheless as good - or even better - than intended. The first paper, published in the latest issue of Nature Biotechnology, is from Mark Styczynski et al. The title is “BLOSUM62 miscalculations improve search performance“. I must say that I was very surprised to see a paper like this. BLOSUM substitution matrices are widely used throughout bioinformatics. In particular the BLOSUM62 version is popular as it is used per default in NCBI’s protein BLAST applications. I am a heavy user of BLOSUM matrices myself; on my computer it is the BLOSUM45 matrix doing mo... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1331519 Thu, 27 Mar 2008 22:37:47 +0100 1331519 http://www.medworm.com/index.php?rid=1321122&cid=t_167197_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F256148742%2F Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. There's a nice quote in the news article from Ste... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1321122 Sat, 22 Mar 2008 18:29:19 +0100 1321122 http://www.medworm.com/index.php?rid=1247908&cid=t_167197_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F238953449%2F David Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 release. (more...) © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under SGRP, genome, genome sequencing, population genomics, resequencing, saccharomyces. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1247908 Thu, 21 Feb 2008 18:50:19 +0100 1247908 http://www.medworm.com/index.php?rid=1196698&cid=t_167197_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F02%2F02%2Fbut-just-before-i-go%2F …I have to mention Carl Zimmer’s post on the quest to find English words in human protein sequences. This game has been around as long as sequence databases have existed. I have a vague memory of a letter from the early 1990s (possibly in Trends in Biochemical Sciences) in which the authors reported the results of comparing SwissProt with the Oxford English Dictionary. As I recall, the longest word that they found was ENSILISTS - meaning people who practice the art of making silage. Anyway - here’s a quick and easy way to tackle the problem using EMBOSS and some Linux command line trickery. Read the rest… (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1196698 Sat, 02 Feb 2008 10:01:42 +0100 1196698 http://www.medworm.com/index.php?rid=1188566&cid=t_167197_132_f&fid=35024&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBlindscientist%2F%7E3%2F226090909%2F From this post I became aware of the paper “Alignment Uncertainty and Genomic Analysis” by Wong et al.. We learn valuable lessons, some evident and some implied. I am covering only the evident here, the implied I leave for the imagination of who’s reading the paper. To the evident lessons (conclusions): Alignments are important for genomics studies Some genes are more difficult to align than others Some alignment programs align some genes better than others, while other alignment programs align other genes better than some Most genes in an organism are under the same DNA model of substitution, hence they all have identical selective pressure, drift, migration, recombination and mutation rates There are things you can only learn from Science. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=1188566 Wed, 30 Jan 2008 20:28:55 +0100 1188566 http://www.medworm.com/index.php?rid=1177731&cid=t_167197_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F223073987%2F WrightFisher talks about a paper & the commentary in Science describing how alignment uncertainty should be taken into account when doing phylogenetic analyses on genomic datastets (some might call this phylogenomics, but Dr Eisen won't). If the sequence alignment is treated as a random variable (and in bayesian approaches have a prior based on result(s) from an alignment program) then more accurate reconstruction. Robin points out several statistical alignment approaches that do just this including TKF91 and recent work that unifies a probabilistic framework with transducers. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1177731 Fri, 25 Jan 2008 18:54:23 +0100 1177731