i-SCORE DESIGNER

The i-Score Designer calculates nine different siRNA designing scores of Ui-
Tei ‚ Amarzguioui‚ Hsieh‚ Takasaki‚ s-Biopredsi‚ i-Score‚ Reynolds‚ Katoh‚ and
DSIR. The nine scores calculated by this service are identical to those
published by individual authors except for s-Biopredsi: The correlation
coefficient of s-Biopredsi and Biopredsi is 0.998. Among the nine different
scores‚ three scores of i-Score. s-Biopredsi‚ and DSIR are classified as the
second generation algorithms that are more dependable than the others. s-
Biopredsi and DSIR are based on 21-mer siRNA sequences‚ but only a 19-mer
segment forming a RNA duplex is shown in the results. Note that there are
no s-Biopredsi and DSIR scores at positions 1 and 2‚ where two additional
nucleotides do not exist at the 5’end. The iScore Designer also calculates the
following parameters:

1. ΔG value of the most stable secondary structure of an siRNA strand

according to the RNA mfold algorithm.
2. Dinucleotide ΔG values at the 5’ and 3’ ends.
3. The ΔG value throughout the siRNA stretch.
4. The maximum length of GC stretch.
5. %GC content.

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CHOPCHOP
CHOPCHOP is a web tool for selecting the optimum target sites for CRISPR/Cas9-
or TALEN-directed mutagenesis.CHOPCHOP can be run with as few as three
basic input options, or with additional advanced parameters. The basic input
comprises:

 A gene name, genomic coordinates or a pasted sequence (including Ref-

Seq and ENSEMBL gene IDs).
 A growing list of organisms.
 The choice between CRISPR/Cas9 or TALEN mode. The advanced options
provide the user with more flexibility when choosing target sites.

Primer X
This software combines design of primers for various PCR applications under
one common platform. The software supports design of degenerate primers on
alignments for amplifying related set of nucleotide sequences for detecting
common traits among organisms and to determine heredity.
The software also designs tagged and nested primers for multiplex
PCR reactions.
The Primer Premier software supports motif analysis and ORF search along with
finding restriction cut sites on the nucleotide sequence.
The software has a built-in nucleotide-protein and protein-nucleotide sequence
translator which can be used for designing degenerate primers for codons that
code for multiple amino acid sequences. It is also understood that the primers
designed by Primer Premier are effective and confirm to the design guidelines
laid for designing primers for housekeeping genes with a high G+C%.
The software also designs primers for flanking exons and introns in a gene,
though there is no mention of it on the official Primer Premier page on
the Premier Bio-soft website.
The software calculates the hairpin structure stability and has been used to
study its effect on PCR amplification.
BioDiscovery Group
Golden Square, 1101, 3rd Floor,
24th Main Rd, 1st Phase,
J P Nagar, Bengaluru,
Karnataka 560078
080 4271 1080, +919538710056
www.biodiscoverygroup.com
NCBI
The National Centre for Biotechnology Information (NCBI) is part of the United
States National Library of Medicine (NLM), a branch of the National Institutes of
Health. The NCBI is located in Bethesda, Maryland and was founded in 1988
through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and
biomedicine and an important resource for bioinformatics tools and services.
Major databases include GenBank for DNA sequences and PubMed, a
bibliographic database for the biomedical literature. Other databases include
the NCBI Epigenomics database. All these databases are available online
through the Entrez search engine.
The program accepts an input sequence, which can be pasted in, picked up from
a local file or retrieved from NCBI as a Genbank file via its accession number. It
calculates all long open reading frames and then displays the sequence, the long
ORFs and all NEB enzymes that cut it just once. It also shows the enzymes which
could be used in a complete digest to excise each open reading frame that it
finds. From the initial display there are options to go further, including custom
digestion with enzymes of your choice and various displays of the digest. One
feature that is implemented on some pages is that moving the mouse over an
enzyme name will produce a box with the recognition sequence and will also
underline the bases of that recognition within the display. On the digest, moving
the mouse on to the bands will display the fragment length and the enzyme that
produced each end of the fragment.

BioDiscovery Group
Golden Square, 1101, 3rd Floor,
24th Main Rd, 1st Phase,
J P Nagar, Bengaluru,
Karnataka 560078
080 4271 1080, +919538710056
www.biodiscoverygroup.com
BLAST
The Basic Local Alignment Search Tool (BLAST) is the most widely used
sequence similarity tool. There are versions of BLAST that compare protein
queries to protein databases, nucleotide queries to nucleotide databases, as
well as versions that translate nucleotide queries or databases in all six frames
and compare to protein databases or queries. PSI-BLAST produces a position-
specific-scoring-matrix (PSSM) starting with a protein query, and then uses that
PSSM to perform further searches. It is also possible to compare a protein or
nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page
at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes
stand-alone BLAST applications for users who wish to run BLAST on their own
machines or with their own databases. This document describes the stand-alone
BLAST applications and will concentrate on the latest generation of such
applications included in the BLAST+ package.

DISCOVERY STUDIO
Discovery Studio is a suite of software for simulating small
molecule and macromolecule systems. It is developed and distributed
by Accelrys.

Oligo Calc
Oligo Calc is a free online calculator to obtain properties of single stranded and
double stranded DNA or RNA sequences. Oligo-Calc provides a user friendly web
interface for calculating the physical properties of oligonucelotides. These
properties include oligonucleotide melting temperature, sequence molecular
weight, %GC content of the entered sequence and absorbance coefficients.

BioDiscovery Group
Golden Square, 1101, 3rd Floor,
24th Main Rd, 1st Phase,
J P Nagar, Bengaluru,
Karnataka 560078
080 4271 1080, +919538710056
www.biodiscoverygroup.com
CLUSTAL W
It is a series of widely used computer programs for Multiple sequence
alignment. There have been many incarnations of Clustal that are listed below:

 Clustal: The original software for progressive alignment based on a

phylogenetic tree.[4]
 ClustalV: A rewrite of the original Clustal package that included phylogenetic
tree reconstruction on the final alignment for the first time.
 ClustalW: command line interface.
 ClustalX: This version has a graphical user interface.
 Clustal Omega: Command line-only program.

BioDiscovery Group
Golden Square, 1101, 3rd Floor,
24th Main Rd, 1st Phase,
J P Nagar, Bengaluru,
Karnataka 560078
080 4271 1080, +919538710056
www.biodiscoverygroup.com