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ATOMS : Bioinformatics ToolBox from DCB details
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Bioinformatics ToolBox from DCB

Basic fuctions for Bioinformatics anlaysis
(137 downloads for this version - 4181 downloads for all versions)
Details
Version
1.1
Author
Umesh P, Deepthi S, Priyadharshini K, Aswathi B L, Vidya R V, Biji C L, Achuthsankar S Nair
Owner Organization
Dept. of Computational Biology & Bioinformatics, University of Kerala, Keralam
Maintainers
Administrator Atoms
P. Umesh
Samuel Gougeon
Categories
License
Creation Date
August 4, 2018
Source created on
Scilab 6.0.x
Binaries available on
Scilab 5.5.x:
Windows 64-bit Windows 32-bit Linux 64-bit Linux 32-bit MacOSX
Scilab 6.0.x:
Windows 64-bit Windows 32-bit Linux 64-bit Linux 32-bit MacOSX
Install command
--> atomsInstall("BTD")
Description
            
BTD: Bio-informatics Toolbox from DCB is a toolbox developed by members of
Department of Computational Biology and Bioinformatics, University of Kerala,
Thiruvananthapuram, Keralam. Various functions have been developed for
processing Nucleotide and Protein sequences. 

Our Project students, Priyadarshini K and Jasmine Russel, and M.Sc students,
Anoop Ambika, Arya S A, Divya D R, Priyanka B R, Sangeetha Jayakumar, Sinumol
George, Sreejith R P and Suresh Kumar, have contributed their academic projects
as functions to the BTD Toolbox.

HELP online PDF
---------------
https://atoms.scilab.org/toolboxes/BTD/1.1/files/Bioinformatics_BTD_1.1_user_manual.pdf


FUNCTIONS
---------
Data bases
- - - - - -
btd_getembl — Gets sequence information from the online EMBL database
btd_getgenbank — Gets sequence information from the online GenBank database
btd_getgenpept — Retrieve sequence information from GenPept database
btd_getpdb — Retrieve protein structure data from Protein Data Bank (PDB)
database
btd_getuniprot — Retrieve sequence information from UniProt database

Conversions
- - - - - -
btd_aa2int — Amino acid to Integers
btd_aa2nt — Amino Acid Sequence to Nucleotide Sequence
btd_dna2rna — DNA sequence to RNA sequence
btd_int2aa — Integer to Amino Acid codes
btd_nt2aa — Nucleotide Sequence to Amino Acid
btd_rna2dna — Convert RNA sequence to DNA sequence

Amino Acids
- - - - - -
btd_aacount — Counts amino acids in sequence
btd_aadensity — Amino Acid Density
btd_atomiccomp — CHONS Atomic Composition of an amino acid sequence
btd_atomicweight — Atomic weight of C,N,O,H,S atoms in an amino acid sequence
btd_avg_hydrophobicity — Average Hydrophobicity of amino acid sequence
btd_basecount — Count nucleotides in a amino acid sequence
btd_cleave — Cleaves amino acid sequence with enzyme
btd_entropyamino — Entropy of Amino Acid
btd_ext_coefficients — Extinction coefficients of aminoacid sequence
btd_exterior_volume — Exterior Volume of amino acid sequence
btd_interior_volume — Interior Volume of aminoacid sequence
btd_lcdensity — Linear Charge Density of an aminoacid sequence
btd_molarabsortivity — Molar absortivity/absorbance of aminoacid sequence
btd_molweigth — Computes the molecular Weight of a amino acide sequence
btd_packingvolume — Volume of Amino Acid Sequence
btd_proteinradius — Radius of Amino Acid Sequence
btd_psv — Partial Specific Volume of a amino acid sequence
btd_volumeratio — Volume Ratio of a amino acid sequence

DNA RNA Nucleotides Misc.
- - - - - - - - - - - - -
btd.nwalign — Needleman-Wunsch Global alignment of two nucleotide sequences
btd.swalign — Smith Waterman Local alignment of two nucleotide sequences
btd_CpG — CpG Islands (counts 'GC' dinucleotides in a DNA sequence)
btd_DNAword — Number and positions of a DNA pattern in a DNA sequence
btd_UpA — UpA Islands : counts 'AU'/'AT' dinucleotides in a DNA/RNA sequence
btd_at2gcratio — AT/GC Ratio
btd_atcontent — AT content of a DNA Sequence
btd_basecomp — Frequency of indicidual nucleotide
btd_codoncount — Count codons in a nucleotide sequence
btd_codonusage — Frequency of each codon type
btd_entropydna — Entropy of DNA
btd_gccontent — Computes the GC content of a DNA sequence
btd_isoelectricpoint — Isoelectric Point
btd_kmer — K-mer counts of number of occurences of given DNA word/substring
btd_ntdensity — Nucleotide Density
btd_purinecomp — Purine Composition of a DNA/RNA sequence
btd_pyrimidinecomp — Pyrimidine Composition
btd_randntseq — Generates a random nucleotide sequence from finite alphabet
btd_randprotseq — Generates a random protein sequence from finite alphabet
btd_rho — Rho
btd_seqcomplement — Complementary strand of a nucleotide sequence
btd_seqrcomplement — reverse complementary strand of a nucleotide sequence
btd_seqshoworfs — Open Reading Frames found in a nucleotide sequence


CHANGES 1.0 => 1.1 
------------------
Full changelog: https://atoms.scilab.org/toolboxes/BTD/1.1/files/changelog.txt

NEW FEATURES
 * btd_getembl, btd_getgenbank, btd_getgenpept, btd_getpdb,
   btd_getuniprot: output filename added in option.

IMPROVED MACROS
* btd_aadensity, btd_ntdensity: plot improved (y<1, AA sequence in title)

BUG FIXED
* btd_getpdb: The URL was wrong (error 404): updated.

JAVA FEATURES
* There were inconsistencies in the class/package/file name.
* Both jimport instructions in btd.nwalign and btd.swalign pages
  were wrong
* ./src/java/loader.sce removed (BTD now does it directly).
NOTE: both btd.nwalign and btd.swalign did not work in v. 1.0:
jimport yielded an error. This may be still the same in v.1.1
(but sometimes it had worked..).

HELP PAGES
* 3 sub-sections created: Amino Acids, Conversions, and Data bases.
* All pages improved a lot. Some are fixed. Please see the full changelog file.

PACKAGING
* builder.sce can now build for both Scilab 5 and Scilab 6
* BDT.start improved
* license_MIT file added
* changelog.txt file added
            
Files (5)
[750.83 kB]
Source code archive

[602.88 kB]
OS-independent binary for Scilab 5.5.x

[685.09 kB]
OS-independent binary for Scilab 6.0.x

[2.07 kB]
Miscellaneous file

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