Anuraj nayarisseri et al, 2012

KodDNA Tutorial

Format Conversion Programs:

EMBL2FASTA– The “EMBL2FASTA” convert your EMBL format to FASTA format. User may input one or more EMBL files and the program quickly removes all of the non-DNA sequence information from the submitted EMBL files and will provide the results in DNA sequence from each EMBL entry.

EMBLFeatureExtrct – The “EMBLFeatureExtrct ” is to procure sequence of cDNA from EMBL genomic flat file data that contains many introns. The program extracts all applicable sequence from a EMBL FLAT file or feature file and will provide the results in FASTA format. User can input one or multiple EMBL FLAT file here.

Genbank2FASTA - The “Genbank2FASTA” convert your GenBank format to FASTA format. User may input one or more GB files and the program quickly removes all of the non-DNA sequence information from the submitted GB file and will provide the results in DNA sequence from each EMBL entry.

GBFeatureExtract - The “GenBank Feature Extractor” is to procure sequence of cDNA from genomic GenBank flat file data that contains many introns. The program extracts all applicable sequence from a GenBank FLAT file or feature file and will provide the results in FASTA format. User can input one or multiple GB FLAT filen here.

Split FASTA– “Split FASTA” convert any FASTA sequence to smaller FASTA sequences. User can specify the size of interest for the same.

Combine FASTA– “Combine FASTA” assist to convert multiple FASTA sequence files into a single fasta sequence file. User may input multiple Gene or Protein sequence in FASTA format here.

Sequence Mapping Programs:

Primer Map– “Primer Map” may use when you have designed a large number of primers for a particular template. Primer Map provides a textual map showing the Restriction endonuclease cut sites, annealing positions of PCR Primers and the protein translations of the DNA sequence.

Restriction Map– “Restriction Map” provides a textual map showing the positions of restriction endonuclease cut sites, the translation of the DNA sequence based on reading frame which user specify. The result of this analysis can be used as a reference when planning cloning strategies.

Translation Map– “Translation map” provides a textual map showing protein translations based on reading frame which user specify or user can choose to treat uppercase text as the reading frame.

Mutate DNA– “Mutate DNA” creates base changes into a DNA sequence. User can select the number of mutations to create, and whether or not to preserve the first and last three bases in the sequence, to reflect selection acting to maintain start and stop codons. The position of each mutation is chosen randomly, and multiple mutations can occur at a single site. The Output mutated DNA sequences can be used to evaluate or a comparative study to understand the significance of sequence analysis.

Mutate Protein - “Mutate Protein” creates amino acid residue changes into a Protein sequence. User can select the number of mutations to create, and whether or not to preserve the first amino acid in the sequence, to reflect selection acting to maintain start codon. The position of each mutation is chosen randomly, and multiple mutations can occur at a single site. The Output mutated Protein sequences can be used to evaluate or a comparative study to understand the significance of sequence analysis.

Prot Align color- Here User can input a group of aligned protein sequences in FASTA format. KodDNA will make and alignment between all protein and colors the alignment. The color is chosen according to the biochemical properties of the amino acid residue. User can specify the percentage of residues that must be identical and similar for the coloring to be applied. User may specify the Color Align Properties to highlight protein regions with conserved biochemical properties.

Sequence Analysis Programs:

ORF Finder - ORF Finder determines the open reading frames (ORFs) in the given DNA sequence. The program “ORF Finder” in KodDNA returns the range of each ORF, along with its protein translation based on reading frame which user specify.

DNA Stats– “DNA Stats” provide the number of occurrences of each nucleotide bases in the DNA sequence. Percentage totals were also given for each nucleotide base, and for certain groups of nucleotide bases, allowing user to quickly compare the results obtained for different sequences.

Protein Stats– “Protein Stats” provide the number of occurrences of each amino acid residues in the Protein sequence. Percentage totals were also given for each residue, and for certain groups of amino acid residues, allowing user to quickly compare the results obtained for different sequences.

Translate DNA– “Translate” program in KodDNA convert a DNA sequence it into a protein in the reading frame based on reading frame which user specify.

Protein GRAVY – Here user can input one or multiple protein sequence of his/her interest. “Protein GRAVY” determines the GRAVY (grand average of hydropathy) value for the protein sequences.

Fuzzy Nuc – User may input a DNA sequence along with a query sequence and KodDNA provides the sites that are identical or similar to the query. Researchers can use this program for finding sequences that can be easily mutated into a useful restriction site.

Fuzzy Pro– User may input a Protein sequence along with a query Amino acid sequence and KodDNA provides the sites that are identical or similar to the query.

Reverse Trans– Here user will have to input a protein sequence.The Program Rev Translate in KodDNA uses a codon usage table to produce a DNA sequence representing the most likely non-degenerate coding sequence. The results will also provide a consensus sequence derived from all the possible codons for each amino acids. KodDNA recommend this program when designing PCR primers to anneal to an unsequenced coding sequence from a related species.

Prot Iso Point - Here user can input one or multiple protein sequence. The program “Prot Iso Point” in KodDNA calculates the theoretical pI (isoelectric point) for the given protein sequence. KodDNA recommends the proteomics researchers for a quick and approximate determination of where on a 2-D gel a particular protein will be found.

Pairwise Prot– “Pairwise Prot” determines the optimal global alignment between 2 Protein sequences. The program Pairwise Prot in KodDNA can be used to perform a Pairwise Alignment between two Protein sequences to look for conserved sequence regions.

Pairwise DNA– “Pairwise DNA” determines the optimal global alignment between 2 DNA sequences. The program Pairwise DNA in KodDNA can be used to perform a Pairwise Alignment between two DNA sequences to look for conserved sequence regions.

Rev. Complnt- Rev. Complnt converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. KodDNA recommends biologists to use Rev. Complnt when an ORF present on the reverse strand.

Prot Patrn srch - User may input one or multiple protein sequences along with a search amino acid pattern and KodDNA provide the number and positions of sites that match the pattern.

DNA Ptrn srch- User may input one or multiple DNA sequences along with a search DNA pattern and KodDNA provide the number and positions of sites that match the pattern.

Idntity & Simlari- Identity and similarity values are requently used to estimate whether or not two sequences share a common ancestor or function. Here user can input a group of aligned sequences (in FASTA or GDE format) and Idntity & Simlari program in KodDNA calculates the identity and similarity of each sequence pair.

CpG Islands - CpG islands or CG islands are genomic regions that contain a high frequency of CpG sites. The "p" in CpG refers to the phosphodiester bond between the cytosine and the guanine, which indicates that the C and the G are next to each other in sequence, regardless of being single- or double- stranded. Here the algorithm for CpG Island Program has been developed based on a 200 bp window moving across the sequence at 1 bp intervals. CpG islands are defined as sequence ranges where the Obs/Exp value is greater than 0.6 and the GC content is greater than 50%. The expected number of CpG dimers in a window is calculated as the number of 'C's in the window multiplied by the number of 'G's in the window, divided by the window length. CpG islands are frequently found in the 5' regions of vertebrate genes, therefore “CpG Islands” Program in KodDNA can be used to highlight potential genes in genomic sequences.

Restriction sites– User can input any DNA sequence of interest. The Program “Restriction sites” in KodDNA Provide the number and positions of commonly used restriction endonuclease cut sites. KodDNA recommends the biologists for quickly determining whether or not an enzyme cuts a particular segment of DNA.

Mutate Digest– User may input a DNA sequence. Here KodDNA searches for regions that can easily be mutated to create a restriction site of interest. The program also reports protein translations so that user can see which reading frames are altered by the proposed mutations. KodDNA Recommend the biologist this program finding sequences that can be converted to a useful restriction site using PCR or site-directed mutagenesis.

Restriction Dig– The “Restriction Digest” Program in KodDNA cleaves a DNA sequence in a virtual restriction digest, with one, two, or three restriction enzymes. The resulting fragments are sorted by size, and they are given a title specifying their length, their position in the original sequence, and the enzyme sites that produced them. User can digest linear or circular molecules and even a mixture of molecules by entering more than one sequence of interest in FASTA format.

DNA Mol Wt– Here user can input one or more DNA sequences. The program “DNA Mol Wt” in KodDNA calculates the molecular weight of the given DNA sequence. Based on the user’s interest, sequences can be treated as double-stranded or single-stranded, and as linear or circular.

Protein Mol Wt– Here user can input one or more Protein sequences. “Protein Mol wt” calculates the molecular weight of the given Protein sequence. Based on the user’s interest, one can attach the copies of commonly used epitopes and fusion proteins using the supplied listed in KodDNA. The program “Protein Mol Wt” in KodDNA may help when the user wish to predict the location of a protein of interest on a gel in relation to a set of protein standards.

PCR Primer St– PCR Primer Stats evaluate potential PCR primers. User may input apts a list of PCR primer sequences by mentioning forward and reverse separated by FASTA format. KodDNA provides a report describing the properties of each primer, including melting temperature, percent GC content, and PCR suitability.

PCR Product– User may input one or multiple DNA sequence templates and two primer sequences. KodDNA searches for perfectly matching primer annealing sites that can generate a PCR product. Output products are sorted by size, and they are given a title specifying their length, their position in the original sequence, and the primers that produced them. User can specify whether the given sequence belongs to linear or circular molecules as the template. KodDNA recommend this programs to biologist to determine the product sizes which expect to see when you perform PCR in the lab.