CMSC 423 Fall 2009: Project SpecificationIntroductionThe project will consist of four components due throughout the semester (see below for timeline). Basic rules:• You are allowed to work in teams of at most 2 people. • The teams can change throughout the semester (i.e. you can work on part 1 with one of your colleagues and on part 2 with another one if you wish). Please clearly indicate on your submission who the members of the team are (both will get the same grade, irrespective of contribution).• You can use any programming language you wish.• Your software must compile and run on the Glue machines so make sure that you test it before submitting it. You can get at most 50% of the grade if we have difficulties compiling or running your code.• The projects must be submitted using the "submit" command on the Glue system. Note: this is different from the "submit server". You must be logged onto glue.umd.edu or linux.grace.umd.edu in order to run the "submit" command.• Your code must be accompanied by a README file that explains the steps necessary to compile and run your project. • 10% of the grade for each component of the project will be awarded for "best programming practices" - make sure your code is neat, well organized and thoroughly commented.Deliverables/Timeline• FASTA parser. Due: 9/17/09 Weight: 10 %• Global alignment of two DNA sequences. Due: 10/13/09 Weight: 10%• Local alignment with affine gap penalties. Due: 10/27/09 Weight: 30%• Overlapper for assembly & incorporation into Minimus assembler. Due: 12/3/09 Weight: 50%Part 1 - FASTA parserDue Thursday, September 17, 2009Overall weight: 10% of total project gradeThe first part of the project requires you to write code that can parse a FASTA file. For this part, you are not allowed to use any of the Bio* libraries available for your programming language of choice. Specification: Your program should read in a FASTA file (sample is available on the Glue system in /class/fall2009/cmsc/423/0101/public/test.fasta) and output a list of sequence identifiers for all sequences that satisfy one of the following:1. are less than 100 bp in length2. contain at least one character that is not A,C,T, or GDetails: • For clarifications on the FASTA format see the Wikipedia entry: http://en.wikipedia.org/wiki/FASTA_format• In addition, you can assume that a sequence identifier follows right after the ">" sign. If a sequence doesn't follow this rule you can exit with an error.• You can also assume that the identifier ends with the first "space" character (space, tab, or end-of-line)• Interface: Your program must accept the input fasta file either through the standard input, or as the only command-line parameter. The output should be provided on standard output.• Any questions about this assignment should be sent to both myself and the TA.Parts 2-4:
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