The 20 June 2008 issue of Science contains a paper by Art Löytynoja and Nick Goldman titled “Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.” The authors tackled the difficult problem of how to handle correctly the placement of insertions and deletions in a multiple sequence alignment. A multiple sequence alignment is typically the input into phylogeny tools that attempt to determine the evolutionary relationship among the sequences. The misplacement of insertions and deletions in a multiple sequence alignment can result misinterpretations of the relationships among the sequences.
Typical multiple sequence alignment tools, such as CLUSTAL W, MUSCLE, MAFFT, and T-COFFEE, do not handle indels accurately. The authors developed new tools, PRANK and PRANK+F, that take into account the computed phylogeny of the sequences when placing insertions and deletions into the multiple alignment.
In this paper, the authors describe their refinements of the multiple alignment algorithm, and they provide theory and results that demonstrate that their algorithm improves the quality of multiple sequence alignments in a biologically meaningful way. The implications of their results are strongest for nucleotide sequence alignments, but the authors contend that their results are important also for peptide sequence alignments.
Source:
Löytnoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632-1635. DOI: 10.1126/science.1158395.
Other bloggers who have have already commented on this paper include:
The Goldman group maintains a web page listing its publications; there are many other interesting papers given there.
June 29 2008 | Bioinformatics | Comments Off
These are my lightly edited tweets for the week of 22 June 2008. Follow me at http://twitter.com/conrad_halling.
- 2008-06-22: Jeff’s wise words in Stack Overflow podcast #10: “Your job as a manager is to throw yourself on grenades to protect me from being interrupted.”
- 2008-06-22: The only earphones worse than the earphones Apple provides with its iPods are the free earphones you get on an airplane.
- 2008-06-22: The Talk Show podcast #22 by John Gruber and Dan Benjamin was devoid of useful content. No transcript available, but none needed.
- 2008-06-26: Yesterday I finished A Deepness in the Sky by Vernor Vinge, a flawless story that is one of the best science fiction novels I’ve read.
- 2008-06-26: Cool technology: The digEplayer you can rent for $10 on long Alaska Airlines flights.
- 2008-06-28: I don’t worry about $4/gal gas. My wife and I have not owned a car for 7 years, since moving to Boston. We use ZipCar: http://zipcar.com/
- 2008-06-28: Another reason we don’t own a car: we can walk to everything. The Walk Score for our neighborhood is 80: http://walkscore.com/
June 29 2008 | Microblog | No Comments »
These are my lightly edited tweets for the week of 15 June 2008. Follow me at http://twitter.com/conrad_halling.
- 2008-06-17: In This Week in Tech #147, John C. Dvorak displays vast ignorance regarding investing or water supply. Can we believe anything he says?
- 2008-06-17: In my search for high-quality science fiction, I have found Vernor Vinge. I’ve started A Deepness in the Sky, which is excellent so far.
- 2008-06-17: I installed Firefox 3 on my MacBook Pro this evening (when I could finally download it). It’s a nice improvement over version 2.
- 2008-06-18: In July, the 8-GB iPhone will cost $199, whereas the 8-GB iPod Touch currently costs $299. I predict a new, lower price for the iPod Touch.
- 2008-06-18: Michael G Schwern has posted his YAPC presentation on skimmable Perl code — lots of good practices.
- 2008-06-20: I’m still reading A Deepness in the Sky by Vernor Vinge. This is a great science fiction book–I’m taking my time so it won’t end too soon.
- 2008-06-20: What I really dislike about the MacBook Pro: The lid doesn’t open as far as it did on the old PowerBook. I can’t get the screen angle right.
- 2008-06-20: In the Firefox 3.0, 2nd bookmark in “most visited” is twitter.com, labeled as “Twitter / Over capacity”. A bug?: I can’t override the label.
June 22 2008 | Microblog | Comments Off
These are my lightly edited tweets for the week of 8 June 2008. Follow me at http://twitter.com/conrad_halling.
- 2008-06-08: I really enjoy the Stack Overflow podcast. But I would never use the Microsoft technologies they advocate.
- 2008-06-09: I spent the day converting some old K&R-format C code to ANSI C. It’s been a long time since I worked with C, but the old skills came back!
- 2008-06-10: @easternblot When I wrote my dissertation, I wrote four hours in the morning, and one or two ours at night. It still took me six weeks.
- 2008-06-12: I’m in Tacoma, Washington, spending the weekend with friends from the Dead Runners Society at DRSWC XVI.
- 2008-06-14: Functional fashion in Seattle now includes the Utilikilt, a heavy kilt with pockets like cargo pants.
- 2008-06-14: Seattle tourist tax: I bought a commuter train ticket in the a.m. to use in the p.m., but they expire after 2 hours — had to buy another.
June 15 2008 | Microblog | Comments Off
These are my lightly edited tweets for the week of 1 June 2008. Follow me at
http://twitter.com/conrad_halling.
- 2008-06-01: Bradley Headstone, the obsessed schoolmaster in Our Mutual Friend by Dickens, is one of the world’s first completely socially inept nerds.
- 2008-06-01: See Rosie Redfield’s Rrresearch blog for a great example of how profiling Perl code showed where to optimize it.
- 2008-06-02: At work, when I redock my Dell Latitude D610, it won’t recognize my new Dell E207WFP 20″ monitor, and I have to reboot. I gotta solve this.
- 2008-06-02: Get “MacOS X Security Configuration for Version 10.5 Leopard“. (Thanks to MacResearch.)
- 2008-06-03: I solved my Dell Latitude D610 vs. Dell E207WFP 20-inch monitor problem by downloading and installing latest Intel graphics video driver.
- 2008-06-03: In this week’s New Yorker, I recommend “The Running Novelist: Learning to Go the Distance”, by Haruki Murakami.
- 2008-06-04: I finished listening to “Our Mutual Friend” by Charles Dickens (40 hrs). This book, although it has its weak parts, is a great work.
- 2008-06-05: The new image of our galaxy, generated by the Spitzer Space Telescope, is now available.
- 2008-06-06: A deficiency of Twitter vs. a blog: you can’t embed URLs. When working with just 140 characters, even tiny URLs can be too long.
- 2008-06-06: My audible.com subscription provides daily news from the Wall Street Journal. Does anyone pay attention to the wrong-headed editorials?
- 2008-06-06: Mailund on the Internet writes about when scientists will want to learn how to program instead of using Excel.
- 2008-06-07: I bought a Sears Craftsman electric weed whacker for cutting my lawn. No internal combustion-created pollution, no gas cans in the cellar.
June 08 2008 | Microblog | Comments Off
These are my lightly edited tweets for the week of 25 May 2008. Follow me at http://twitter.com/conrad_halling.
- 2008-05-25: I finished “The Mind Readers”. The mystery wasn’t mysterious, the science fiction wasn’t science, and Albert Campion wasn’t interesting.
- 2008-05-25: Like many other science geeks, I’m watching coverage of the Mars Phoenix lander…. Only 33 minutes until the first signal will be received.
- 2008-05-25: @MarsPhoenix Congratulations on a successful landing!
- 2008-05-26: On Sunday, June 1, the American Society for Microbiology annual meeting begins here in Boston. Lots of good sessions, including genomics.
- 2008-05-27: Software I use daily: Circus Ponies Notebook. http://www.circusponies.com/.
- 2008-05-28: Does anyone get excited over getting a new Dell Latitude laptop computer? The pedestrian design of Dell laptops bores me.
- 2008-05-28: Today I learned that it is impossible to do bioinformatics when the network is down. I hope the new card for our router arrives tomorrow.
- 2008-05-29: Mac OS X 10.5.3 update for my six-month old MacBook Pro: An enormous download (420 MB) and three reboots. Everything is fine so far.
- 2008-05-29: New 21st-centry prize for science: The Kavli prize (http://www.kavliprize.no/), awarded in astrophysics, nanoscience, and neuroscience.
- 2008-05-29: Congratulations, California, on legalizing same sex marriage. Signed — a proud resident of Massachusetts, where same sex marriage is legal.
- 2008-05-30: John Gruber explained Spaces in Mac OS X 10.5.3 (http://daringfireball.net/2008/05/spaces). Now I’m ready to use this feature.
- 2008-05-31: 90% of my computer activity is work-related, so I don’t take much time to have fun. But today I set up Spaces and played with Photo Booth.
- 2008-05-31: I played more on my MacBook today. GarageBand is a lot of fun. Now I want to buy a USB keyboard. But tomorrow it’s back to serious work.
June 01 2008 | Microblog | Comments Off
