New Informatics Club on Campus

There is a new student organization on the Indiana University Southeast campus!

The IUS Informatics Club was founded in December of 2008 and will be holding its first meeting on Thursday, January 29th from 1 - 2 PM in the UC 127 conference room. Any Informatics or Computer Science student is welcome to attend, as well as anyone interested in either of those fields.

The subjects to be discussed will be what students would like to get out of the club, the possibility of entering into an employment database based out of Bloomington, and the future meeting times of the organization.

For those who cannot make the first meeting, a followup meeting will take place the following Wednesday. The time and place of that meeting, as well as its content, will be worked out later, and when that information is available it will be posted.

BiRG Christmas Cake

Our BiRGer 'Mark' surprised me today when he walked into the BiRG lab with a big cake. Here are the photos of the cake and the BiRG lab.

Thank you very much for the cake! A very Merry Christmas and a very Happy New Year to you all.

IU School of Informatics named to Computerworld's top IT schools to watch

BLOOMINGTON, Ind. -- Computerworld magazine announced in its August 2008 issue its "Top IT Schools to Watch 2008," and the Indiana University School of Informatics was among the 10 schools recognized in a feature article on graduate programs.

The schools, including institutions such as Carnegie Mellon University, Stanford University, the University of Pennsylvania, and the University of Virginia, were selected based on how well they were keeping pace with today's IT workplace, and the relevance of their curriculum to the ever-changing technology industry.

IU's School of Informatics was touted for not only providing students with real-world experience, but for its interdisciplinary approach to the field and for the responsiveness of its faculty and the students.

The list was compiled by a panel of more than two dozen IT executives, hiring managers, recruiters and academics who were asked to help identify the country's leading-edge schools for IT workers seeking to advance their careers. They considered graduate-level IT programs and schools that give graduates the best value in terms of salary increases or promotions vs. cost of tuition, and that best gear their curriculum to the everyday demands of today's IT workplace.

From the IT schools selected by the panel, Computerworld editors chose the innovative IT schools to profile. Finally, Computerworld partnered with Dice.com to survey alumni at the schools, asking for feedback on their satisfaction with their schools' program.

"We are honored to be part of Computerworld's list for 2008," said Bobby Schnabel, dean of the School. "It is gratifying to be in the company of schools that have long been considered at the top of the computing field, and to gain recognition for our still young set of graduate programs in informatics."

The complete story can be found in the August issue of ComputerWorld magazine and online at www.computerworld.com.

Founded in 2000 as the first school of its kind in the United States, the Indiana University School of Informatics is dedicated to research and teaching across a broad range of computing and information technology, with emphases on science, applications, and societal implications. The school includes the Departments of Computer Science and Informatics on the Bloomington campus and Informatics on the IUPUI campus.

The school administers a variety of bachelor's and master's degree programs in computer science and informatics, as well as Ph.D. programs in computer science and the first-ever doctorate in informatics. The School is dedicated to excellence in education and research, to partnerships that bolster economic development and entrepreneurship, and to increasing opportunities for women and underrepresented minorities in computing and technology. For more information, visit www.informatics.indiana.edu.

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Re: Speed Museum Membership

Note that IU Southeast is an institutional member of the Speed Art Museum in Louisville for 2008.  This membership entitles faculty members, staff, and students to free admission to the museum's permanent art collection, special traveling exhibitions, AfterHours events, and selected lectures and concerts.  You must show your IU Southeast ID card to take advantage of this membership.

BiRG minutes: 7-18-2008

Comparing Two Sequences

 Objectives:

•          Get the basics about dot plots

•          Know how to interpret the most common patterns in a dot plot

•          Use Dotlet

•          Use Lalign to extract local alignments

 
Why compare two?

•          Database searches are useful for finding homologues

•          Database searches don't provide precise comparisons

•          More precise tools are needed to analyze the sequences in detail including

–        Dot plots for graphic analysis

–        Local or global alignments for residue/residue analysis

•          The alignment of two sequences is called a pairwise alignment

 
Dot Plot:

•          A dot plot is a graphic representation of pairwise similarity

•          The simplicity of dot plots prevents artifacts

•          Ideal for looking for features that may come in different orders

•          Reveal complex patterns

•          Benefit from the most sophisticated statistical-analysis tool in the universe . . . your brain

 
Choosing your two sequences:

•          Making pairwise comparisons takes time

•          Use BLAST to rapidly select your sequences

–        More than 70% identity for DNA

–        More than 25% identity for proteins

•          If your sequences are too similar, comparing them yields no useful information

 What can you analyze with Dot Plot?

•          Any pair of sequences

–        DNA

–        Proteins

–        RNA

•          DNA with proteins

–        Dotlet is an appropriate tool

–        To compare full genomes, install the program locally

•          Sequences longer than 1000 symbols are hard to analyze online

 •          Divergent sequences where only a segment is homologous

•          Long insertions and deletions

•          Tandem repeats

The square shape of the pattern is characteristic of these repeats

Using Dotlet:

•          Dotlet is one of the handiest tools for making dot plots

•          Dotlet is a Java applet

•          Open and download the applet at the following site:

–        www.isrec.isb-sib.ch/java/dotlet

•          Dotlet slides a window along each sequence

•          If the windows are more similar than the threshold, Dotlet prints a dot at their intersection

•          You can control the similarity threshold with the little window on the left

•          Every dot has a score given by the window comparison

•          When the score is

–        Below threshold 1                           ó black dot

–        Between thresholds 1 and 2       ó grey dot

–        Above threshold 2                           ó white dot

•          The blue curve is the distribution of scores in the sequences

•          The peak ó most common score,

–        Most common ó less informative

•          Window size and the stringency control the aspect of your dot plot

–        Very stringent = clean dot plot, little signal

–        Not stringent enough = noisy dot plot, too much signal

•          Play with the threshold until a usable signal appears

 
•          The square shape is typical of tandem repeats

•          The repeats are not perfect because the sequences have diverged after their duplication

Comparing a Gene and its Product:

•          Eukaryotic genes are transcribed into RNA

•          The RNA is then spliced to remove the introns' sequences

•          It may be necessary to compare the gene and its product

•          Dotlet makes this comparative analysis easy

 
Aligning Sequences:

•          Dotlet dot plots are a good way to provide an overview

•          Dot plots don't provide residue/residue analysis

•          For this analysis you need an alignment

•          The most convenient tool for making precise local alignments is Lalign

 Lalign and BLAST:

•          Lalign is like a very precise BLAST

•          It works on only two sequences at a time

•          You must provide both sequences

 
Going Farther:

•          If you need to align coding DNA with a protein, try these sites:

–        www.tcoffee.org => protogene

–        coot.embl.de/pal2nal

•          If you need to align very large sequences, try this site:

–        www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi

•          If you need a precise estimate of your alignment's statistical significance, use PRSS

–        The program is available at fasta.bioch.virginia.edu

–        Low E-value ó good alignment

BiRG Minutes : June 11, 2008

Analyzing Protein Sequences

 In-silico biochemistry

 Sliding-windows techniques – most ancient way of looking at sequences

                -used if the strand of DNA was cut in the middle

                -ND THE WAS where the A was cut off

                                NDT HEW AS

                                DTH EWA S

                                THE WAS

                -Use past experiences and what proteins have been together in the past

-Hydrophobicity is the most popular analysis – a good indicator of transmembrane segments or core regions within a protein.

 
Predicting transmembrane domains

ProtScale allows one to compute and represent the profile produced by any amino acid scale on  a selected protein.

amino acid scale is defined by a numerical value assigned to each type of amino acid.

THMM Transmembrane Helix Prediction is a method for predicting transmembrane helices based on a hidden Markov Model (HMM)

HMM - a statistical model in which the system being modeled is assumed to be a Markov process with unknown parameters, and the challenge is to determine the hidden parameters from the observable parameters. The extracted model parameters can then be used to perform further analysis, for example for pattern recognition applications.

THMM creates a prediction, or what it should have been

ProtScale has parameters and shows what it is

Predicting post-translational modifications w/PROSITE

                Proteins get modified between the cell and getting read

                PROSITE motifs are written as patterns

–      Short patterns are not very informative by themselves

–      They only indicate a possibility

–      Combine them with other information to draw a conclusion

NOT EVERYTHING IS IN PROSITE

                Interpreting PROSITE patterns

                                Some patterns may suggest nonexistent protein features

                                Short patterns are more informative if they are conserved across homologous sequences

Domains is defined as " independent globular folding units".  It is a portion of protein that can keep its shape if you remove it from the rest of the protein.  It consists of at least 50 amino acids.  -  Domains are like the various components of our kitchen – such as the oven, the microwave, the refrigerator, etc.  All together they constitute the complete kitchen, but they can also exist separately.  You only need to use microwave when making pop corn - which can be done outside the kitchen.

An average protein consists of 2 or 3 domains.  Usually each domain plays a specific role in the function of the protein.  It  may interact with other proteins, or bind ion like calcium or zinc, or it may contain an active site.  It is common to have a catalytic domain associated with a binding domain and a regulatory domain.   Imagine -   a toaster, where you have the grill [catalytic], the toast holder [binding], and the switch [regulation].

Domains are like independent functions that can be taken out of a program but still function

Researchers

A domain is a multi-sequence alignment similar to a puzzle

Using Domain collections

Scientists have been discovering and characterizing protein domains for more than 20 years

Manual collections are precise but small; where the researchers must document everything on their own

Automatic collections go out and find data in research documents etc

It is probably that only one of these servers will have the information to help you understand your protein

Meeting Minutes: 27th June 2007

We welcomed our newest BiRG member "Kimberly Holmes"
The discussion today was about Working with a single DNA sequence : the slides are available in the Shared Folder
David began his presentation with the statement "Not everything that can be counted counts and not everything that counts can be counted"

Topics covered in detail included

- PCR
- Cloning
- Cleaning a DNA sequence (removing contamination)
- Restriction Map
- FIRTSMARKET website (use Netscape browser)
- Primer Design (MIT Website)
- Emboss
- Gene Prediction [ prokaryotes -> GeneMark ]
- Gene Prediction [ eukaryotes -> Genomescan ]
- BLAST
- Shotgun sequencing/contigs/assemble/homology
- read pieces
- PHRAP assembly program
- CAP3 program for joining small sequences

We have a nice discussion with Dr. Ramachandran explaining several concepts during the presentation. We also discussed about gene expression and Hidden Markov Models

Lastly, we do not meet next week - Independence Day - July 4