Comparative Analysis of Structure and Sequences of Oryza sativa Superoxide Dismutase
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species (ROS).
2. Materials and Methods
In this study bioinformatics tools, software and methods
were used for the sequences comparison of Oryza sativa
SODs. This includes sequence retrieval, local BLAST
database creation and BLAST search, BioEdit, Port-Pa-
ram tool, MEGA phylogenetic tree construction, ANTH-
EPORT-SOPMA, SWISS-MODEL, YASARA, PRO-
CHECK-COMP, Ramachandran plot analysis and PTF
database.
2.1. Sequence Retrieval
In order to analyze protein sequences and structures the
amino acids sequences of the protein of interest is most
essential. Protein sequences can be searched from a vari-
ety of protein primary sequence databases viz. (PIR,
MIPS, SWISS PROT, TrEMBL, NRL-3D [9] (Attwood
and Parry-Smith, 2002)). SWISS-PROT/TrEMBL data-
base used for retrieving the amino acid sequences of
Oryza sativa SODs. SWISS-PROT is an annotated pro-
tein sequence database established in 1986 and main-
tained collaboratively by the Swiss Institute for Bioin-
formatics (SIB) and the European Bioinformatics Insti-
tute (EBI). The data in SWISS-PROT are derived from
translations of DNA sequences from the EMBL nucleo-
tide sequence database, adapted form the Protein Identi-
fication Resource (PIR) collection, extracted from the
literature and directly submitted by researchers. TrEMBL,
a computer-annotated supplement to SWISS-PROT, ac-
companies SWISS-PROT. Amino acids sequences of
Oryza sativa SODs were retrieved from SWISS-PROT/
TrEMBL available at www.expasy.org.
2.2. Sequence/Primary Structure Analysis
The exact nature of the information encoded in primary
structure is still unclear. Detailed fold ing studies have re-
vealed more and more complexities, making it under-
stand that the sequence to structure relation is a very
complicated problem. Using sequence analysis techni-
ques, attempt was made to identify similarities between
novel query sequence and database sequences, whose
structures and functions have been elucidated. The straight
forward at high levels of sequence identity, where rela-
tionships are distinctly clear, but below 50% identity it
becomes increasingly difficult to establish relationships
reliably [8].
2.2.1. Local BLAST
Local BLAST has been created by using BioEdit. Local
BLAST (Basic Local Alignment Search Tool) search is
often used as the most convenient method for detecting
homology of a biological sequence to existing character-
ized sequences. Local BLAST looks for homology by
searching for locally aligned regions of identity and
similarity between a query sequence in a local database.
Local BLAST database was created by using file con-
taining all the sequences of Oryza sativa SODs in
FASTA format. In BioEdit, from the “Accessary applica-
tion” menu “BLAST” was chosen. Then ‘Create local
database’ was selected. The rest of the things were auto-
matic. The database automatically placed into the data-
base folder for the BioEdit install directory. This local
BLAST has been used to find out the sequence similarity
between Oryza sativa SODs. The query sequence of
every SODs were given to local BLAST for BLAST
search against all Oryza sativa SODs that were present in
the local BLAST databases.
2.2.2. Pr otParam
ProtParam is a tool, which allows the computation of
various physical and chemical parameters for a given
protein stored in SWISS-PROT or TrEMBL for a user
entered sequence. The computed parameters include the
molecular weight, theoretical isoelectric point (pI),
amino acid composition, atomic composition, extinction
coefficient, estimated half-life, instability index, alip hatic
index and grand average of hydropathicity (GRAVY).
The protein can be specified as a SWISS-PROT of TrE-
MBL accession number or ID or in the form of raw se-
quence. If the accession number of a SWISS-PROT or
TrEMBL entry is provided, then we prompt with an in-
termediary page that allows selecting the portion of the
sequence on which analysis is to be performed. The
choice includes a selection of mature chains or peptides
and domains from the SWISS-PROT/TrEMBL table, as
well as the possibility to enter start and position in two
boxes. By default the complete sequence will be ana-
lyzed. PortParam tool has been used for analyzing phy-
siochemical properties of Oryza sativa SODs. The amino
acids sequence of Oryza sativa SODs in FASTA format
were given to ProtParam tool available at www.expasy.
org. The physiochemical properties of Oryza sativa
SODs were given.
2.2.3. BioEdit
BioEdit is a biological sequence editor that runs in Win-
dows and is intended to provide basic functions for pro-
tein and nucleic sequence editing, alignment, manipula-
tion and analysis. Hydrophobic amino acids tend to occu r
in the interior of globular proteins, while at the surface of
a protein one will preferen tially find hydroph ilic residues.
The hydrophobicity scale or related scale are frequently
used for the prediction of antigenic epitopes. Mean hy-
drophibicity profiles are generated using the general
method of Kyte-Doolitte. Kyte-Doolitte compiled a set of
“hydropathy scores” for the 20 amino acids based upon
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