Protein Record Database
Contents
1. will not store any complete protein records in memory aside from the particular one that is being used at any given time Program Invocation The program will take the names of three files from the command line like this ProteinDB lt database file name gt lt command script file name gt lt log file name gt If the database file is not found open a new file using the given name and begin execution with an empty database Naturally if the script file is not found the program should log an error message and exit Data and File Structures There will be an initial database file in the format described earlier Adding a new protein record to the database requires updating the indexing data structures in memory as well as the initial database file on disk Each of the search keys is simply an ASCII string and so the keys can be compared using the standard relational operators The accession codes are unique primary that is no two different proteins will have the same accession code None of the other fields are guaranteed to be primary The index structure for the accession codes will be stored using a binary search tree The index entries in the accession code index will store the accession code and the corresponding record locator of the corresponding protein record in the dB file A record locator is a non negative integer specifying the file offset at which the record begins The index for the source organisms will also be store2. CS 2605 Project 3 Spring 2008 Protein Sequence Database A protein is a large molecule manufactured in the cell of a living organism to carry out essential functions within the cell The primary structure of a protein is a sequence of amino acids There are 20 common amino acids each of which has a chemical name e g Glycine a three letter abbreviation e g Gly and a one letter code e g G See http www chemie fu berlin de chemistry bio amino acids_en html for a table about the chemistry of the amino acids and http courses cs vt edu algnbio genetic_code index php for information about how the amino acids fit into the genetic code The twenty one letter codes are A C D EH Ey G H I K Ly M Ny P QO Re S Ty Vy WX For the purpose of representing and manipulating the primary structure of a protein it suffices to use the one letter codes in a string For example MLOSIIKNIWIPMKPYYTKVYOE IWIGMGLMGFIVYKIRAADKRSKALKASAPAPGHH is the amino acid sequence for a human protein called 6 8 kDa mitochondrial proteolipid In this project amino acid sequences will always be upper case with no white space inserted There are many online databases from which protein sequences can be obtained One is SWISS PROT which can be found at http ca expasy org sprot As of March 27 2004 SWISS PROT contained database entries for 146 720 amino acid sequences Each database entry has much more information about a protein than i
3. TTAT CNTADOKYCG GTWQGIIDKL DYIQGMGFTA IWITPVTAQL POTTAYGDAY HGYWQQDIYS LNENYGTADD LKALSSALHE RGMYLMVDVV ANHMGYDGAG SSVDYSVFKP FSSQDYFHPF CFIQNYEDQT QVEDCWLGDN TVSLPDLDTT KDVVKNEWYD WVGSLVSNYS IDGLRIDTVK HVOQKDFWPGY NKAAGVYCIG EVLDGDPAYT CPYQNVMDGV LNYPTYYPLL NAFKSTSGSM DDLYNMINTV KSDCPDSTLL GTFVENHDNP RFASYTNDIA LAKNVAAFII LNDGIPIITYA GQEQHYAGGN DPANREATWL SGYPTDSELY KLIASANATIR NYAISKDTGF VTYKNWPIYK DDTTIAMRKG TDGSQIVTIL SNKGASGDSY TLSLSGAGYT AGQQLTEVIG CTTVTVGSDG NVPVPMAGGL PRVLYPTEKL AGSKICSSS In the sample above some the DE and SQ lines have been wrapped to fit the width of the page In the data file those would occur on a single line CS 2605 Project 3 Spring 2008 Assignment You will implement a system that maintains a database of amino acid sequences proteins stored in the format described above There is no stated limit on the number of records that may be in the file so all data structures must be fully dynamic Your system will build and maintain several in memory index data structures to support the following operations Retrieving protein records from the database file based on the accession code Retrieving protein records from the database file based on source organism Displaying the in memory indices in a human readable manner You will implement a single C program to perform all system functions Note that your program
4. d using a BST but there may be many protein records that match a single organism The source organism index will store index entries containing the organism name and a collection of corresponding primary accession codes NOT record locators This means that retrievals based on the source organism name will require first searching the source organism index and then performing one or more searches of the primary accession code index Aside from where specific data structures are required you may and should take advantage of any suitable STL component you like At the start of execution your program should parse the database file and build both index structures Each index object should have the ability to write a nicely formatted display of itself to an output stream Other System Elements You are expected to apply the object oriented design principles you were taught in the prerequisite courses when designing the system The following discussion is intended only to provide food for thought It is highly probable that there are other expected design elements that are not mentioned here CS 2605 Project 3 Spring 2008 There should be an overall controller that validates the command line arguments and manages the initialization of the indices The controller should hand off execution to a command processor that manages retrieving commands from the script file and making the necessary calls to other system elements which will then carry out tho
5. goals of this assignment include but are not limited to creation of a sensible OO design for the overall system including the identification of a number of useful classes not explicitly named in this specification implementation of such an OO design into a working system incremental testing of the basic components of the system in isolation satisfaction when the entire system comes together in good working order Pledge Each of your program submissions must be pledged to conform to the Honor Code requirements for this course Specifically you must include the pledge statement provided on the Submitting Assignments page of the course website
6. ncise protein record field specifications Each line begins with a two character line code which indicates the type of data contained in the line The line code is always followed by exactly three spaces The line types and line codes that may appear in a concise entry are shown in the table below Line code Content Occurrence in an entry Comments DE Description foneme SSCS os ormer Optional zero ormore eC Comments ornoves Optional zero or more SSS so seauencedsta Joe id i Termination ine Oncesendstheenty SSS As shown in the table some line types are found in all entries others are optional Some line types occur many times in a single entry Each entry ends with a terminator line Note that some formatting details must be inferred from the sample data files provided on the course website and the detailed documentation available online in the UniProt User Manual Note that there are absolutely no stated limits on the lengths of the strings that occur in the protein records CS 2605 Project 3 Figure 1 Sample Concise Protein Record Spring 2008 AC P10529 DE Alpha amylase A precursor EC 3 2 1 1 Taka amylase A TAA 1 4 alpha D glucan glucanohydrolase Os Aspergillus oryzae KW Carbohydrate metabolism Hydrolase Glycosidase Calcium binding KW Signal Glycoprotein Multigene family 3D struc
7. se commands Index entries are objects So are protein records An index is more than just a naked container Command File The execution of the program will be driven by a script file Lines beginning with a semicolon character are comments and should be ignored Each non comment line of the command file will specify one of the commands described below Each line consists of a sequence of tokens which will be separated by single tab characters A newline character will immediately follow the final token on each line The command file is guaranteed to conform to this specification so you do not need to worry about error checking when reading it The following commands must be supported display lt tab gt lt accession gt Log the complete protein record that has primary accession code lt accession gt describe lt tab gt lt accession gt Log the description field in the protein record that has primary accession code lt accession gt Do not log the complete record organism lt tab gt lt species gt Log the accession code and file offset for every protein record that includes the organism name given in lt species gt At the end of the list log the number of matching protein records that were found Do not log the records themselves debug lt tab gt accession organism Log the contents of the specified structure in a fashion that makes the internal structure and contents of the index clear It is not necessary to be overly verbo
8. se here but it would be useful to include information like key values file offsets and record lengths where appropriate exit lt tab gt Terminate program execution A sample command script is included in Figure 2 below As a general rule every command should result in some output In particular error messages should be logged if searches yield no protein records Instrumentation Each index or its aggregated container must be instrumented so that it logs information about each search it performs The information should display each index record that is accessed during the index search and should be written to the log file Note that this information will be used to assess the correctness and performance of your data structures so if you don t do this you should expect major deductions CS 2605 Project 3 Spring 2008 Figure 2 Sample Command Script Test script for protein database project Display initial indices debug accession debug organism r Describe a few records describe 058489 describe 057577 i Display a few records display 058489 display 057577 i Remove a few sequences remove 058489 remove 027743 i Find a few organisms organism Methanopyrus kandleri organism Aeropyrum pernix r Quit exit File Navigation Performing some of the search functions in this assignment requires being able to move to an arbitrary location in the database file This is ea
9. sy to do if you make use of the appropriate features of C stream objects Every input stream maintains an internal data member that stores the current position of the input pointer called the get pointer within the file The value of the get pointer is just the offset in bytes of the current position from the beginning of the file Bytes are numbered sequentially starting at zero just like the cells of an array The get pointer moves forward automatically when the usual input operations are performed on the stream object The current position of the get pointer can be obtained by calling the member function tellg on the stream object The get pointer can be moved to an arbitrary offset within the file by calling the member function seekg and passing it the specified file offset Log File Description Since this assignment will be graded by TA rather than the Curator the format of the output is left up to you Of course your output should be clear concise well labeled and correct The remainder of the log file output should come directly from your processing of the command file You are required to echo each command that you process to the log file so that it s easy to determine which command each section of your output corresponds to Each command should be numbered starting with 1 and the output from each command should be well formatted and delimited from the output resulting from processing other commands A complete sample log
10. ts sequence as can be seen by going to http ca expasy org cgi bin get full entry SWISS_PROT ID 68MP_HUMAN This is the entry for the protein whose sequence was given above A complete protein record may contain a fairly large number of logical fields These are flagged with two character sequences occurring at the beginning of each line A full listing of the possible fields is given in Table 1 on page 2 of this specification It is important to note that some protein records will contain only a proper subset of the possible fields In addition the amount of data for each field can vary considerably For our purposes in this assignment we will use a text file of modified shortened SWISS PROT entries You do not need to be concerned with validating the correctness of the database entries A full description of the logical significance of the various fields and any format constraints is given in the UniProt User Manual which is available at http us expasy org sprot userman html Table 1 below describes the fields that are present in the shortened records we will be using Figure 1 below shows a sample shortened protein record Note some of the sequence data files may contain multiple entries corresponding to the same accession code In such a case your implementation should recognize if an accession code is already in the index structure and if so simply reject the duplicate entries CS 2605 Project 3 Spring 2008 Table 1 Co
11. ture CC CATALYTIC ACTIVITY Endohydrolysis of 1 4 alpha glucosidic CE linkages in oligosaccharides and polysaccharides GE COFACTOR Binds 2 calcium ions per subunit Calcium is inhibitory Ce at high concentrations CE SUBUNIT Monomer CE BIOTECHNOLOGY Used in the brewing industry to increase the CC fermentability of beer worts including those made from unmalted CE cereals in the starch industry to make high maltose and high DE CC syrups starch saccharification in the alcohol industry to CC reduce fermentation time in the cereal food industry for flour CC supplementation and improvement of chilled and frozen dough and CC in the forestry industry for low temperature modification of CC starch Sold under the name Fungamyl by Novozymes CC MISCELLANEOUS The sequence of AMY1 and AMY2 is shown Ge SIMILARITY Belongs to family 13 of glycosyl hydrolases CC CC This SWISS PROT entry is copyright It is produced through a collaboration ee between the Swiss Institute of Bioinformatics and the EMBL outstation CC the European Bioinformatics Institut There are no restrictions on CC use by non profit institutions as long as its content is in no EC modified and this statement is not removed Usage by and for commercial CC ntities requires a license agreement S http www isb sib ch announce GE or send an email to license isb sib ch CE SQ MMVAWWSLFL YGLQVAAPAL AATPADWRSQ SIYFLLTDRF ARTDGS
12. will be posted shortly on the course website CS 2605 Project 3 Spring 2008 Submitting Your Program You will submit this assignment to the Curator System read the Student Guide where it will be archived for grading by a TA For this assignment you must submit a zip file containing all the source code files for your implementation 1 e header files and cpp files Submit only the header and cpp files Submit nothing else In order to correct submission errors and late breaking implementation errors you will be allowed up to five submissions for this assignment You may choose which one will be evaluated at your demo but we will evaluate only one submission The Student Guide and link to the submission client can be found at http www cs vt edu curator Evaluation Note that the evaluation of your project will depend substantially on the quality of your code and documentation See the Programming Standards page on the course website for specific requirements that should be observed in this course You will generally not be allowed to make any changes to your submitted code during a project demo If the TA determines that it is not possible to fairly evaluate your submission without allowing you to make changes he will document the changes that you make and I will assess a penalty for those changes The penalty will never be less than the equivalent of a one day late penalty and will usually be more Pedagogic points The
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