{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2025-12-14T01:33:56.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2025-12-14T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":811,"title":"Genome Sequence 004: Long 3rd Generation Segment Correction","description":"The Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003chttp://www.pacificbiosciences.com/ PacBio\u003e. The \u003chttp://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar Assemblathon Genome Contest\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003chttp://www.sciencedaily.com/releases/2012/07/120702210229.htm Sequence Parrot DNA\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\r\n\r\nThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u003c1% error rate. Jarvis and his team combined this data to achieve \u003c 0.1% error rate.\r\n\r\nGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\r\n\r\n*Input:* \r\n\r\nCall 1: empty array, segment Width, Flag=0\r\n\r\nCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\r\n\r\n*Output:* \r\n\r\nCall 1: empty vector, Number of Requested Vectors\r\n\r\nCall 2: Corrected DNA vector, Number of Requested Vectors\r\n\r\n*Score:* Number of N vectors used to produce correct vector for w=1024 case\r\n\r\nThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\r\n\r\nThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\r\n\r\nThe response to the second call is the fixed DNA sequence, vector of width w.\r\n\r\n*example:*\r\nFirst call return : N=3\r\n\r\n  01230123111122223333 Truth\r\n  Input example\r\n  01232123112122221332 Injected errors\r\n  01130123111122123323\r\n  11230133121122223333\r\n\r\n  Output: \r\n  01230123111122223333 Truth, hopefully\r\n\r\n\r\nThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned. \r\n\r\nThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\r\n\r\nFollow-Up Challenges: Sample Data from the PacBio site for \u003chttp://www.cbcb.umd.edu/software/PBcR/ Lambda Phage\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\r\n","description_html":"\u003cp\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003ca href=\"http://www.pacificbiosciences.com/\"\u003ePacBio\u003c/a\u003e. The \u003ca href=\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\"\u003eAssemblathon Genome Contest\u003c/a\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003ca href=\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\"\u003eSequence Parrot DNA\u003c/a\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/p\u003e\u003cp\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/p\u003e\u003cp\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty array, segment Width, Flag=0\u003c/p\u003e\u003cp\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003e\u003cb\u003eScore:\u003c/b\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/p\u003e\u003cp\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/p\u003e\u003cp\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/p\u003e\u003cp\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/p\u003e\u003cp\u003e\u003cb\u003eexample:\u003c/b\u003e\r\nFirst call return : N=3\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003e01230123111122223333 Truth\r\nInput example\r\n01232123112122221332 Injected errors\r\n01130123111122123323\r\n11230133121122223333\r\n\u003c/pre\u003e\u003cpre class=\"language-matlab\"\u003eOutput: \r\n01230123111122223333 Truth, hopefully\r\n\u003c/pre\u003e\u003cp\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/p\u003e\u003cp\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/p\u003e\u003cp\u003eFollow-Up Challenges: Sample Data from the PacBio site for \u003ca href=\"http://www.cbcb.umd.edu/software/PBcR/\"\u003eLambda Phage\u003c/a\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/p\u003e","function_template":"function [M_fix,N]=PacBio_fix(M,w,flag)\r\n% 1st Call\r\n% M is empty\r\n% w is width of segment\r\n% flag is 0\r\n% Ouput is N, the number of segments requested to fix the segment\r\n% 2nd Call\r\n% M is an Nxw array of values [0:3]\r\n\r\n M_fix=[];\r\n N=1; % needed for 2nd call with flag==1\r\n if flag==0 % Requested number of Segments\r\n  N=1;\r\n  return;\r\n end\r\n\r\nM_fix=M(1,:);\r\n\r\n\r\nend","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\nM=[];\r\nflag=0;\r\nw=100;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n%%\r\nM=[];\r\nflag=0;\r\nw=6144;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\n%%\r\n% Size Performance is based on w=1024 case\r\nM=[];\r\nflag=0;\r\nw=1024;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,not_N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\nfeval(@assignin,'caller','score',min(20,N));\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2012-10-08T02:30:34.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T05:26:57.000Z","updated_at":"2012-10-08T02:40:09.000Z","published_at":"2012-10-08T02:29:50.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.pacificbiosciences.com/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ePacBio\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e. The\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAssemblathon Genome Contest\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e led the team of Phillippy, Koren and Jarvis to successfully\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eSequence Parrot DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty array, segment Width, Flag=0\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScore:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eexample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e First call return : N=3\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[01230123111122223333 Truth\\nInput example\\n01232123112122221332 Injected errors\\n01130123111122123323\\n11230133121122223333\\n\\nOutput: \\n01230123111122223333 Truth, hopefully]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eFollow-Up Challenges: Sample Data from the PacBio site for\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.cbcb.umd.edu/software/PBcR/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eLambda Phage\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":811,"title":"Genome Sequence 004: Long 3rd Generation Segment Correction","description":"The Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003chttp://www.pacificbiosciences.com/ PacBio\u003e. The \u003chttp://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar Assemblathon Genome Contest\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003chttp://www.sciencedaily.com/releases/2012/07/120702210229.htm Sequence Parrot DNA\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\r\n\r\nThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u003c1% error rate. Jarvis and his team combined this data to achieve \u003c 0.1% error rate.\r\n\r\nGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\r\n\r\n*Input:* \r\n\r\nCall 1: empty array, segment Width, Flag=0\r\n\r\nCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\r\n\r\n*Output:* \r\n\r\nCall 1: empty vector, Number of Requested Vectors\r\n\r\nCall 2: Corrected DNA vector, Number of Requested Vectors\r\n\r\n*Score:* Number of N vectors used to produce correct vector for w=1024 case\r\n\r\nThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\r\n\r\nThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\r\n\r\nThe response to the second call is the fixed DNA sequence, vector of width w.\r\n\r\n*example:*\r\nFirst call return : N=3\r\n\r\n  01230123111122223333 Truth\r\n  Input example\r\n  01232123112122221332 Injected errors\r\n  01130123111122123323\r\n  11230133121122223333\r\n\r\n  Output: \r\n  01230123111122223333 Truth, hopefully\r\n\r\n\r\nThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned. \r\n\r\nThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\r\n\r\nFollow-Up Challenges: Sample Data from the PacBio site for \u003chttp://www.cbcb.umd.edu/software/PBcR/ Lambda Phage\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\r\n","description_html":"\u003cp\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003ca href=\"http://www.pacificbiosciences.com/\"\u003ePacBio\u003c/a\u003e. The \u003ca href=\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\"\u003eAssemblathon Genome Contest\u003c/a\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003ca href=\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\"\u003eSequence Parrot DNA\u003c/a\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/p\u003e\u003cp\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/p\u003e\u003cp\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty array, segment Width, Flag=0\u003c/p\u003e\u003cp\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003e\u003cb\u003eScore:\u003c/b\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/p\u003e\u003cp\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/p\u003e\u003cp\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/p\u003e\u003cp\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/p\u003e\u003cp\u003e\u003cb\u003eexample:\u003c/b\u003e\r\nFirst call return : N=3\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003e01230123111122223333 Truth\r\nInput example\r\n01232123112122221332 Injected errors\r\n01130123111122123323\r\n11230133121122223333\r\n\u003c/pre\u003e\u003cpre class=\"language-matlab\"\u003eOutput: \r\n01230123111122223333 Truth, hopefully\r\n\u003c/pre\u003e\u003cp\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/p\u003e\u003cp\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/p\u003e\u003cp\u003eFollow-Up Challenges: Sample Data from the PacBio site for \u003ca href=\"http://www.cbcb.umd.edu/software/PBcR/\"\u003eLambda Phage\u003c/a\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/p\u003e","function_template":"function [M_fix,N]=PacBio_fix(M,w,flag)\r\n% 1st Call\r\n% M is empty\r\n% w is width of segment\r\n% flag is 0\r\n% Ouput is N, the number of segments requested to fix the segment\r\n% 2nd Call\r\n% M is an Nxw array of values [0:3]\r\n\r\n M_fix=[];\r\n N=1; % needed for 2nd call with flag==1\r\n if flag==0 % Requested number of Segments\r\n  N=1;\r\n  return;\r\n end\r\n\r\nM_fix=M(1,:);\r\n\r\n\r\nend","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\nM=[];\r\nflag=0;\r\nw=100;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n%%\r\nM=[];\r\nflag=0;\r\nw=6144;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\n%%\r\n% Size Performance is based on w=1024 case\r\nM=[];\r\nflag=0;\r\nw=1024;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,not_N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\nfeval(@assignin,'caller','score',min(20,N));\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2012-10-08T02:30:34.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T05:26:57.000Z","updated_at":"2012-10-08T02:40:09.000Z","published_at":"2012-10-08T02:29:50.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.pacificbiosciences.com/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ePacBio\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e. The\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAssemblathon Genome Contest\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e led the team of Phillippy, Koren and Jarvis to successfully\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eSequence Parrot DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty array, segment Width, Flag=0\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScore:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eexample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e First call return : N=3\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[01230123111122223333 Truth\\nInput example\\n01232123112122221332 Injected errors\\n01130123111122123323\\n11230133121122223333\\n\\nOutput: \\n01230123111122223333 Truth, hopefully]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe real PacBio data is quite a bit more complicated. 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