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Kansas State University

Bioinformatics

 

Blast
Fingerprinting
Fragment Analysis
Sequence Analysis
Alignment of Sequence Pairs
Multiple Sequence Alignment
Genomic DNA-mRNA Alignment
Gene Prediction
Repeat Identification
Primer Designing
SNP Analysis
QTL Analysis
Functional Annotation
Translate Inverse Tool

 

  1. Blast :



    2.      NCBI

         DFCI Wheat Genome

         Wheat Genome Database

         Rice Genome Annotation

         EST BLAST HITS

         Wheat SNP Database

     

     

  2. Fingerprinting :



    3.      Genemapper4.0

         GenoProfiler 2.0

         FPC (FingerPrinted Contig)

         Tutorial of Image (The Fingerprint image analysis System)

         Web FPC Tool

         FPMiner2.0

         FPPipeliner2.0

         Internet Contig Explorer(iCE)

     

     

  3. Frgament Analysis :


    4.      Genemapper4.0

     

     

  4. Sequence Analysis :


    5.      Sequence Scanner Spftware v1.0

         Sequencher

         Genetool Lite:

     

     

  5. Alignment of Sequence Pairs :


    6.      BCM Search Launcher: Pairwise sequence alignment

         Global Alignment program

     

     

  6. Multiple Sequence Alignment :


    7.      T-COFFEE

         ClustalW @ EBI

     

     

  7. Genomic DNA-mRNA Alignment :


    8.      Spidey

         SIM4 - cDNA and Genomic DNA Alignment

         MGAlignIt

     

     

  8. Gene Prediction :


    9.      Gene Scan

         FGENESH

     

     

  9. Repeat Ientification :


    10.      RepeatMasker

         Censor (GIRI)

         TIGR Plant Repeat Database

     

     

  10. Primer Designing :


    11.     Primer3

     

     

  11. SNP Analysis:


    12.      Sequence Scanner SoftwareV1.0

         Sequencher4.8

         SNPmasker

         PARSESNP

     

     

  12. QTL Analysis :


    13.      Qgene4

      

     

     

  13. Functional Annotation :


    14.      Blast2go

         AmiGo

     

     

     

  14. Translate / Inverse Tool :


    15.      Translate

         TranslatER

         Reverse, Compliment, Inverse