The group is both computational and experimental.

We ask biological questions to large datasets made using novel genomics techniques, with the help of computers. One of the strengths in the group are the many connections to high-profile experimental laboratories which supply data to be analyzed.

Lab webpage @ http://people.binf.ku.dk/albin/Sandelin_group_at_the_Bioinformatic_Centre/The_Sandelin_group.html

* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
* Feature/Model Learning: developing algorithms and software

Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

http://research.janelia.org/peng/

In C, "sequence statements" are imperatives. The "selection" is the "if then else" statement, and the iteration is satisfied by a number of statements, such as the "while," " do," and the "for," while the case-type statement is satisfied by the "switch" statement.

Pseudocode is an artificial and informal language that helps programmers develop algorithms. Pseudocode is a "text-based" detail (algorithmic) design tool.

The rules of Pseudocode are reasonably straightforward. All statements showing "dependency" are to be indented. These include while, do, for, if, switch. Examples below will illustrate this notion.

GUIDE TO PSEUDOCODE LEVEL OF DETAIL: Given record/file descriptions, pseudocode should be created in sufficient detail so as to directly support the programming effort. It is the purpose of pseudocode to elaborate on the algorithmic detail and not just cite an abstraction.

Examples:

1.

If student's grade is greater than or equal to 60
    Print "passed"
else
    Print "failed"  
endif

2.

  
Set total to zero
Set grade counter to one
While grade counter is less than or equal to ten
    Input the next grade
    Add the grade into the total
endwhile 
Set the class average to the total divided by ten
Print the class average.

3.

Initialize total to zero
Initialize counter to zero
Input the first grade
while the user has not as yet entered the sentinel
   add this grade into the running total 
   add one to the grade counter  
   input the next grade (possibly the sentinel)
endwhile

if the counter is not equal to zero
   set the average to the total divided by the counter
   print the average  
else
   print 'no grades were entered' 
endif 

4.

initialize passes to zero
initialize failures to zero
initialize student to one
while student counter is less than or equal to ten
    input the next exam result  
    if the student passed

add one to passes else add one to failures add one to student counter endif endwhile print the number of passes print the number of failures if eight or more students passed print "raise tuition" endif

5.

Larger example:  

NOTE:  NEVER ANY DATA DECLARATIONS IN PSEUDOCODE

Print out appropriate heading and make it pretty
While not EOF do:
     Scan over blanks and white space until a char is found 
	(get first character on the line)
     set can't-be-ascending-flag to 0
     set consec cntr to 1
     set ascending cntr to 1
     putchar first char of string to screen
     set read character to hold character
     While next character read != blanks and white space
          putchar out on screen
          if new char = hold char + 1
               add 1 to consec cntr
               set hold char = new char
               continue
          endif
          if new char >= hold char 
               if consec cntr < 3 
                    set consec cntr to 1
               endif
               set hold char = new char
               continue
          endif
          if new char < hold char
               if consec cntr < 3
                    set consec cntr to 1
               endif
               set hold char = new char
               set can't be ascending flag to 1
               continue
           endif
     end while
     if consec cntr >= 3 
          printf (Appropriate message 1 and skip a line)
          add 1 to consec total
     endif
     if  can't be ascending flag = 0
          printf (Appropriate message 2 and skip a line)
          add 1 to ascending total
     else
          printf (Sorry message and skip a line)
          add 1 to sorry total
     endif
end While
Print out totals:  Number of consecs, ascendings, and sorries.
Stop

Some Keywords That Should be Used And Additional Points

For looping and selection, The keywords that are to be used include Do While...EndDo; Do Until...Enddo; While .... Endwhile is acceptable. Also, Loop .... endloop is also VERY good and is language independent. Case...EndCase; If...Endif; Call ... with (parameters); Call; Return ....; Return; When;

Always use scope terminators for loops and iteration.

As verbs, use the words Generate, Compute, Process, etc. Words such as set, reset, increment, compute, calculate, add, sum, multiply, ... print, display, input, output, edit, test , etc. with careful indentation tend to foster desirable pseudocode. Also, using words such as Set and Initialize, when assigning values to variables is also desirable.

More on Formatting and Conventions in Pseudocoding

• INDENTATION in pseudocode should be identical to its implementation in a programming language. Try to indent at least four spaces.
• As noted above, the pseudocode entries are to be cryptic, AND SHOULD NOT BE PROSE. NO SENTENCES.
• No flower boxes (discussed ahead) in your pseudocode.
• Do not include data declarations in your pseudocode.
• But do cite variables that are initialized as part of their declarations. E.g. "initialize count to zero" is a good entry.

  ---

  Function Calls, Function Documentation, and Pseudocode
• Calls to Functions should appear as:
• Returns in functions should appear as:
• Function headers should appear as:
• Note that in C, arguments and parameters such as "fieldn" could be written: "pointer to fieldn ...."
• Functions called with addresses should be written as:
• Function headers containing pointers should be indicated as:
• Returns in functions where a pointer is returned:
• It would not hurt the appearance of your pseudocode to draw a line or make your function header line "bold" in your pseudocode. Try to set off your functions.
• Try to use scope terminators in your pseudocode and source code too. It really hels the readability of the text.

  ---

  Source Code
• EVERY function should have a flowerbox PRECEDING IT. This flower box is to include the functions name, the main purpose of the function, parameters it is expecting (number and type), and the type of the data it returns. All of these listed items are to be on separate lines with spaces in between each explanatory item.
• FORMAT of flowerbox should be

   

  	 ********************************************************
  	 Function:   ( cryptic text describing single function
  		     ....... (indented like this) 	
  		     .......
  	 Calls:      Start listing functions "this" function calls
  		     Show these functions:  one per line, indented
  
  	 Called by:  List of functions that calls "this" function
  		     Show these functions:  one per line, indented.
  
  	 Input Parameters:  list, if appropriate; else None
  	 
  	 Returns:    List, if appropriate.
  	 ****************************************************************
  

• INDENTATION is critically important in Source Code. Follow standard examples given in class. If in doubt, ASK. Always indent statements within IFs, FOR loops, WILLE loops, SWITCH statements, etc. a consistent number of spaces, such as four. Alternatively, use the tab key. One or two spaces is insufficient.
• Use scope terminators at the end of if statements, for statements, while statements, and at the end of functions. It will make your program much more readable.

  SPELLING ERRORS ARE NOT ACCEPTABLE

Position Paper Submission Extension: October 9, 2014 
Regular Paper Authors Notification: November 3, 2014 
Position Paper Authors Notification: November 6, 2014 
Regular and Position Paper Camera Ready and Registration: November 17, 2014 

Address of the bookmark: http://www.bioinformatics.biostec.org/

Address of the bookmark: http://scikit-bio.org/

Perl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like Inkscape and Abobe Illustrator(R).

The input file must be a text file with at least the marker name (ID), linkage group (LG) and the position (POS) separeted by tabulations. Additionally a logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.

map.tsv

ID<tab>LG<tab>POS<tab>LOD
13519  12     0       0.250840894
2718   12     1.0     0.250840893
11040  12     1.6     0.252843341
...

https://github.com/pseudogene/genetic-mapper

Address of the bookmark: https://github.com/pseudogene/genetic-mapper

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

This project presents demonstrations of selected computer science algorithms important in bioinformatics, implemented in the spreadsheet program Microsoft Excel. Spreadsheets provide an interesting platform for demonstration of algorithms, since various steps of the calculations can be exposed in a manner that is easily comprehensible to users with little programming experience. The algorithms demonstrated include two approaches to approximate string matching (dynamic programming and Shift-AND numeric approximate matching), Hierarchical Clustering (used in phylogenetic studies and microarray analysis of gene expression), a Naive Bayes Classifier for simulated microarray gene expression data, and a simple Neural Network. These demonstrations are designed to serve as instructional aids in bioinformatics courses.

Tutorial @ http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsInExcel.zip

One of the best resource for online bioinformatics learning is https://stepic.org/Bioinformatics-Algorithms-2 Enjoy the online learning.

Reference : cybertory

" Please add your favourite bioinformatics algorithms and tutorial links below in the comment section, for the benefit of bioinformatics and computational biology community ". 

Address of the bookmark: http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf