A site of software resources.  -since C.E.2009-

If you want to access to a past information before Nov 2, 2020 then you can access to following archive.
http://web.archive.org/web/20201102001521/https://sites.google.com/site/kashiwagiakihiro/

 1.LCS with GUI - 2024/7/11 21:07 updated

 2.Freeware NEKO11

 3.Jazz Music by MagicGarageBand

 4.At Nuclear Energy Library

 5.PLM/PMBOK Overview

-Holy Scriptures Bible

 4.How to effective use The Watch Tower Library

 5.How to make card of the bible text

 6.My favorite texts of bible

 7.A Note of "Flavius Josephus's Books of the History of the Jewish War against the Romans."

-Bioinformatics

 8.LCS(Longest Common Subsequence) of Dynamic Programming No.1

 9.Spectral Convolution

10.Coin Probability Graph - Coffee break -

11.Cuts at stop codon

12.Extract ORF

13.Confirm the extracted sequence No.1

14.Confirm the extracted sequence No.2

15.Calculate probability to amino acid in gene

16.Fine adjustment for a program - Coffee break -

17.Confirm the extracted sequence No.3

18.LCS(Longest Common Subsequence) of Dynamic Programming No.2

19.Reverse sequence of nucleotide and integration in the past programs - Coffee break -

20.Local alignment and affine gap penalty

21.Verification to abstracted ORF No.1

22.Verification to abstracted ORF No.2

23.Modify to LCS

24.A problem of find motif

25.A problem of find motif by tree structure

26.LCS with GUI - 2024/7/11 21:07 updated

27.Compared to enzymes

28.A explanation for the butterfly operation of FFT - Coffee break

29.Confirm the extracted sequence No.3

30.About a speedup the finding motif probrem by the CUDA

31.A Multi threading for LCS of Dynamic Programming

32.How to compare a transition probability of HMM

33.The six phases Deep Neural Network

34.About how to calculate Back propagation

35.About how to calculate Restricted Boltzmann Machine

36.DNA Recognizer by using Neural Network - Block and Flow chart

37.Gene prediction by using Neural Network  

38.An Introduction to Backpropagation with GPU

-Motif of Mycoplasma Genitalium - 2020/10/24  Update!

39.lmer 9 frequencies 3

40.lmer 9 frequencies 100

41.lmer 9 frequencies 100 of mapping on GeneMarkHMM 26m

42.lmer 9 frequencies 106

43.lmer 9 frequencies 116

44.lmer 9 frequencies 129

45.lmer 9 frequencies 132

46.lmer 9 frequencies 148

47.lmer 15 frequencies 3

48.lmer 15 frequencies 8

49.lmer 36 frequencies 6

50.lmer 48 frequencies 6

-Files of docking Simulation of RNA Polymerase of SARS Corona Virus2 and Ivermectin - 2022/4/28 New !

-A docking Simulation of Papain-Like Protease of SARS Corona Virus2 (6w9c) and Ivermectin (ivm) - 2020/6/10

51.Simulation 1.  movie    pse for pymol    2020.5.21

52.Simulation 2.  movie    pse for pymol    2020.5.26

53.Simulation 3.  movie    pse for pymol    2020.5.26

-A docking Simulation of RNA Polymerase of SARS Corona Virus2 (7bzf) and Ivermectin (ivm) - 2020/6/20 

54.Ligand Ivermectin(IVM)    pdbqt for Autodoc Vina    2020.6.14

55.Rigid RNA Polymerase(7bzf chain A)    pdbqt for Autodoc Vina    2020.6.11

56.Flex RNA Polymerase(7bzf chain A)    pdbqt for Autodoc Vina    2020.6.11

57.Autodoc Vina Input File    2020.6.11

58.Simulation 1.  movie    pse for pymol    Output File    Log    2020.6.11

59.Simulation 2.  movie    pse for pymol    Output File    Log    2020.6.14

60.Simulation 3.  movie    pse for pymol    Output File    Log    2020.6.15 a

61.Simulation 4.  movie    pse for pymol    Output File    Log    2020.6.15 b

62.Simulation 5.  movie    pse for pymol    Output File    Log    2020.6.15 c

63.Simulation 6.  movie    pse for pymol    Output File    Log    2020.6.15 d

64.Simulation 7.  movie    pse for pymol    Output File    Log    2020.6.15 e

65.Simulation 8.  movie    pse for pymol    Output File    Log    2020.6.16 a

66.Simulation 9.  movie    pse for pymol    Output File    Log    2020.6.16 b

67.Simulation 10.  movie    pse for pymol    Output File    Log    2020.6.16 c

68.Simulation 11.  movie    pse for pymol    Output File    Log    2020.6.17 a

-High Score Result about docking simulation of  RNA Polymerase of SARS Corona Virus2 (7bzf) and Ivermectin (ivm) - 2020/8/30 

69.Ligand Ivermectin(IVM)    pdbqt for Autodoc Vina    2020.6.14

70.Rigid RNA Polymerase(7bzf chain A)    pdbqt for Autodoc Vina    2020.8.13

71.Flex RNA Polymerase(7bzf chain A)    pdbqt for Autodoc Vina    2020.8.13

72.Autodoc Vina Input File    2020.8.13

73.Simulation.  movie    pse for pymol    Output File    Log    2020.8.20 New! - This is high score result -11.5[kcal/mol]

74.Simulation.  movie    pse for pymol    Output File    Log    2020.8.20a

75.Simulation.  movie    pse for pymol    Output File    Log    2020.8.23

-GitHub repository

    https://github.com/a-kashiwagi/bioinformatics-tools

99.About Akihiro

私文書偽造等罪: 3月以上5年以下の懲役 電磁的記録不正作出及び共用罪: 5年以下の懲役または50万円以下の罰金

信用毀損罪: 虚偽の風説を流布し、又は偽計を用いて、人の信用を毀損する犯罪

業務妨害罪: 虚偽の風説を流布し、又は偽計を用いて、人の業務を妨害すること（偽計業務妨害罪）または威力を用いて人の業務を妨害すること（威力業務妨害罪）