We have developed BBH-Toolkit for the students and researchers to perform basic analysis with sequences/data. This is the first step to learn the bioinformatics research. Afterwords, the students can perform different kind of advanced analysis with different type of datasets.

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seqlen.pl

This Perl script seqlen.pl calculates the length of the sequence.

USAGE:

-i : User can provide file containing multiple DNA, RNA or protein sequences in the FASTA format as input using this option.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and calculates the length of the sequence.

• It stores the output in a user specified file.

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codonusage.pl

This Perl script codonusage.pl computes percentage of each nucleotide bases such as Adenine(A), Guanine(G), Cytosine(C),Thymine(T) and Uracil(U) in the given nucleotide sequences.

 It also calculates AT/AU and GC content for each nucleotide sequences.

USAGE:

-i : User can provide file containing multiple DNA or RNA sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output can be stored using this option.

DESCRIPTION:

• This program receives input from the user and calculates the percentage of each nucleotide bases.

• It also calculates the AT\AU and GC content for the given nucleotide sequences present in a file.

• It stores the output in a user specified file.

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dnamotif.pl

A DNA motif is a nucleic acid sequence pattern that has some biological significance. Motifs are candidates for functionally important sites. This program dnamotif.pl checks the presence of user specified motif in the given set of DNA sequences.

USAGE:

-i : User can provide file containing multiple DNA sequences in the FASTA  format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and checks the user specified motif in the given set of nucleotide sequences.

• It stores the output in a user specified file.

 

protmotif.pl

Motifs are the candidates for functionally important sites. Presence of a motif can be used as a base of protein classification. This program protmotif.pl checks the presence of user specified motif in the given set of protein sequences.

USAGE:

-i : User can provide file containing multiple protein sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and checks the user specified motif in the given set of protein sequences.

• It stores the output in a user specified file.

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promw.pl

Certain modifications to this protein sequences can result in changes to the molecular weight of the protein. Based on the molecular weight of the protein, we can easily list out the protein that comes under the same molecular weight. This program promw.pl calculates the molecular weight of protein from the given protein sequences.

USAGE:

-i : User can provide file containing multiple protein sequences in the FASTA  format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and calculates the molecular weight of the protein from the protein sequences.

• It stores the output in a user specified file.

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nonnuc.pl

N bases in sequence data generally means the software is unable to identify the base. N bases may appear at the beginning of the sequence result for a number of reasons. Poor data produces wrong results. Analyzing the poor data takes more CPU time and produce wrong interpretation.

nonnuc.pl program removes the non-nucleotide character N in the given DNA sequences or RNA sequences.

USAGE:

-i : User can provide file containing multiple DNA or RNA sequences in the FASTA  format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and removes the non-nucleotide character N in the given DNA sequences or RNA sequences.

• It stores the output in a user specified file.

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dnamw.pl

This program calculates the molecular weight of Single Stranded RNA (ssRNA) or  Single Stranded (ssDNA) and Double Stranded DNA (dsDNA) from the given nucleotide sequences.

USAGE:

 -i : User can provide file containing multiple nucleotide sequences in the FASTA format as input using this option.

 -o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and calculates the molecular weight of ssRNA orssDNA and dsDNA from the given nucleotide sequences.

• It stores the output in a user specified file.

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translate.pl

Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis. This program translate.pl converts DNA or RNA sequences to protein sequence.

USAGE:

-i : User can provide file containing multiple DNA or RNA sequences in the FASTA format as input using this option.

-o : User can specify the file in which output need to be stored using this option.

Description:

• This program receives input from the user and translates the DNA or RNA sequences to protein sequence.

• It stores the output in a user specified file.

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transcribe.pl

Transcription is the process by which the information in a strand of DNA is copied into a new molecule of mRNA. Conversion of DNA sequences to mRNA sequences act as a genetic code. This genetic code is used to construct a functional product such as protein. Sequence editors cannot convert multiple DNA sequences into multiple RNA sequences. This program transcribe.pl converts multiple DNA sequences to multiple RNA sequences.

USAGE:

-i : User can provide file containing multiple DNA  sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and transcribes the DNA sequences to RNA sequences.

• It stores the output in a user specified file.

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onetothree.pl

Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. Three letter code amino acids can be used as simple text as well as the original reports of experimental details of sequences. It is suitable for reporting the details of peptide synthesis. It helps to represent the specific amino acids of the protein sequences in a triple letter code. This program onetothree.pl converts amino acids represented in single letter code to triple letter code in the protein sequences.

USAGE:

-i : User can provide file containing multiple protein sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output can be stored using this option.

DESCRIPTION:

• This program receives input from the user and converts amino acids represented in single letter code to triple letter code in the protein sequences.

• It stores the output in a user specified file.

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trimends.pl

Trimming of the sequences from the ends is also an important tasks in several bioinformatics operations. This perl script trimends.pl trims poor quality data from the ends of sequences. Therefore it removes low quality regions and vector contamination.

This program trims the user specified region in the input molecular sequences.

USAGE:

-i : User can provide file containing multiple molecular sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

-s : User can specify starting location of the region needed to be trimmed using this option.

-e : User can specify ending location of the region needed to be trimmed using this option.

DESCRIPTION:

• This program receives input from the user and trims the end of the multiple FASTA sequences.

• It stores the output in a user specified file.

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triminbetween.pl

This Perl script triminbetween.pl removes the bases (user specified region) in between the sequences.

USAGE:

-i : User can provide file containing multiple molecular sequences in the FASTA format as input using this option.

-o : User can specify the file in which output need to be stored using this option.

DESCRIPTION:

• This program receives input from the user and it will trim in between the multiple FASTA sequences.

• It stores the output in a user specified file.

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primer.pl

A primer can be defined as short nucleic acid sequences. It can act as a starting point for DNA synthesis.  In order to produce the desired DNA sequence, you must start with the right primer. This program primer.pl predicts forward and reverse primer for Polymerase Chain Reaction using the given DNA sequences.

USAGE:

-i : User can provide file containing multiple DNA sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

-f : User can specify the length of the forward primer using this option.

-r : User can specify the length of the reverse primer using this option.

DESCRIPTION:

• This program receives input from the user and predicts forward and reverse primer for Polymerase Chain Reaction using the given DNA sequences.

• It stores the output in a user specified file.

 

region.pl

The region of promoter, terminator, introns, and exons from the sequences have been extracted using this script. This Perl script extract user specified position from the multiple FASTA sequences and stored it in a user specified output file. This program region.pl provides the user specified region in the input DNA sequences.

USAGE:

-i : User can provide file containing multiple DNA sequences in the FASTA format as input using this option.

User can also provide raw sequences as input but all the sequences will be considered as a single sequence.

-o : User can specify the file in which output need to be stored using this option.

-s : User can specify starting location of the region needed using this option.

-e : User can specify ending location of the region needed using this option.

DESCRIPTION:

• This program receives input from the user and extracts the user specified region from the input multiple FASTA sequences.

• It stores the output in a user specified output file.

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