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Future Research

S. Future Research. Zemin Ning. Future Research:. (1) Individual Bioinformatics Tools:. (i) Sequence alignment and cross-genome comparison ;. (ii) WGS assembler – including EST clustering and Assembly. (iii) SNP Detection – ssahaSNP2 .

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Future Research

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  1. S Future Research Zemin Ning

  2. Future Research: (1) Individual Bioinformatics Tools: (i) Sequence alignment and cross-genome comparison; (ii) WGS assembler – including EST clustering and Assembly (iii) SNP Detection – ssahaSNP2 (iv) SsahaEST – an EST alignment tool for gene prediction and analysis (2) Analysis Server - GenomeTask

  3. Sequence Alignment and Cross-genome Comparison SSAHA -> SSAHA2 -> SSAHA3 -> SSAHA4 SSAHA2 = SSAHA + Cross_match SSAHA3 = SSAHA + Blast SSAHA4 = Cross-genome comparison

  4. Mapping - Cross-genome Comparison SUBJECT Q U E R Y

  5. Local Alignment Sub -Subject S u b | Q u e r y Smith-Waterman Or modified Smith-Waterman

  6. Assembly Data Process Shotgun Reads Supercontig FPC Mapping Read-pair Tracker PRono RPjoin –Merge Reads Group RPphrap - Contig Phusion Assembler Pipeline

  7. Phusion – Reads Grouping

  8. Phusion – Other Parts Making Phrap really aware of read-pairs? Making Phrap handle indels more properly? Better read placement file; Better supercontig structure.

  9. SSAHA seeds EST reads Edge length Edge length Sequence for cross_match Genomic Sequence ssahaEST Prediction of Splice Sites

  10. ssahaSNP2 The weakness of ssahaSNP: (1) Multi-read alignment; (2) Detecting indels; ssahaSNP2: During the process of developing SSAHA2, I have successfully changed the memory allocation utilities in the phrap/cross_match system. It is therefore possible to combine ssaha with phrap to make a mini-assembly in the local areas and to detect high quality base discrepancies as SNPs or insertions/deletions due to polymorphisms.

  11. Client Various Tools www Server FTP site GenomeTask GenomeTask (Genome Tools and Analysis Station Kit) is a client/server system, which hosts a number of informatics tools under one roof. Its function is to provide services to the community for analyzing genomic data in large quantities.

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