Molecular Systematics of Nematodes - Russian Journal of Nematology

Molecular Systematics of
Nematodes
Databases and BLAST
Sergei A. Subbotin
Department of Nematology, University of California, Riverside, USA,
Gent University, Gent, Belgium
Center of Parasitology, Russian Academy of Sciences, Moscow, Russia

DataBase
The one of the most important things
in molecular biology: the comparison
of data sequenced by yourself with all
known sequences collected in a
certain database. This procedure is
called homology search. Numerous
genetic databases are spread out all
over the world. The probably biggest
nucleic acid databases are:
http://www.embl-heidelberg.de/
http://www.ncbi.nlm.nih.gov/
http://www.nig.ac.jp/

GenBank

GenBank
NCBI Resources NCBI (National Center
for Biotechnology Information) is a
resource for molecular biology
information. NCBI creates and maintains
public databases, conducts research in
computational biology, develops software
tools for analyzing genome data, and
disseminates biomedical information.
The NCBI site is constantly being
updated and some of the changes
include new databases and tools for data
mining.
NCBI offers several searchable literature,
molecular and genomic databases and
many bioinformatic tools. An up-to-date
list of databases and tools can be found
on the NCBI Sitemap.
Location: www.ncbi.nlm.nih.gov

GenBank
from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months

GenBank
NCBI Sitemap

GenBank

Entrez
•Entrez: Entrez is a retrieval system
designed for searching several linked
databases of the NCBI for the major
databases, including PubMed, Nucleotide
and Protein Sequences, Protein Structures,
Complete Genomes, Taxonomy, and others.
. Entrez categories can be searched using
subject, author, or unique identifiers such
as accession numbers, phrases, truncated
terms, and combined sets. There is also a
simple Entrez tutorial.

GenBank
PubMed: Allows searching
by author names, journal
titles, and a new
Preview/Index option.
PubMed database provides
access to over 12 million
MEDLINE citations back to
the mid-1960's. It includes
History and Clipboard
options which may
enhance your search
session. NCBI provides a
simple PubMed tutorial.

PubMed
Search : Perry RN

GenBank
Nucleotide Database: The
nucleotide database contains
sequence data from GenBank,
EMBL, and DDBJ, the members
of the tripartite, international
collaboration of sequence
databases. Nucleotide allows the
user to retrieve nucleotide
sequences in both GenBank and
FASTA formats.
The Entrez Nucleotide database
is a collection of sequences from
several sources, including
GenBank, RefSeq, and PDB. The
number of bases in these
databases continues to grow at an
exponential rate. As of April 2006,
there are over 130 billion bases in
GenBank and RefSeq alone.

GenBank
Taxonomy Database: The
taxonomy database contains
the names of all organisms
that are represented in the
genetic databases with at
least one nucleotide or
protein sequence. You can
search for nucleotide, protein,
and structure data from
specific taxonomic groupings,
from the domain level
(archaea,
bacteria,
eukaryota) down to the
species level.

GenBank
Taxonomy Browser is…
browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
• taxonomy information such as genetic codes
• molecular data on extinct organisms
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

Taxonomy Browser

Blast (Sequence Similarity Search)
BLAST: BLAST (Basic
Local Alignment Search
Tool) is a set of similarity
search programs
designed to explore all of
the available sequence
databases regardless of
whether the query is
protein or DNA. For a
better understanding of
BLAST you can refer to
the BLAST Course which
explains the basics of the
BLAST algorithm, or to
the NCBI BLAST tutorial.
http://www.ncbi.nlm.nih.gov/BLAST/

Blast (Sequence Similarity Search)
Sequence alignments provide a
powerful way to compare novel
sequences with previously
characterized genes. Both
functional and evolutionary
information can be inferred from
well designed queries and
alignments. BLAST 2.0, (Basic
Local Alignment Search Tool),
provides a method for rapid
searching of nucleotide and
protein databases.
BLAST - the most popular datamining
tool ever!
For non-coding DNA - use blastn.
Never forget that blastn is only for
closely related DNA sequences
(more than 70 percent identical).

Blast (Sequence Similarity Search)
1. Point your browser to the NCBI BLAST
server
at:
http://www.ncbi.nlm.nih.gov/BLAST
2. Under the Nucleotide heading, click the
Nucleotide-Nucleotide (blastn) link
3. Paste your sequence in the search
window
4. Click Blast! button
5. Click Format button (and wait)
An overview of the BLAST output
1. A graphic display: Shows you where
your query is similar to other sequences
2. A hit list: The name of sequences
similar to your query, ranked by
similarity
3. The alignments: Every alignment
between your query and the reported
hits
4. The parameters: A list of the varios
parameters used for the search

Blast (Sequence Similarity Search)
The graphic display
• Your query sequence in on the top
• Each bar represents the portion of another
sequence similar to your query sequence
• Red bars indicate the most similar sequences,
pink bars indicate matches that are a bit less
good, and green bars indicate matches that
are not impressive at all. Blue and black hits
(not here) are bad hits
The hit list
Each line contains four important features:
• The sequence accession number and the
names: this hyperlink takes you to the
database entry that contains this sequence
• Description
• The bit score: a measure of the statistical
significance of the alignment. The higher the
bit score, the more similar the two sequences.
Matches below 50 bits are very unreliable
• The E-value (the expectation value): by
estimating the number of times you could
have expected such a good much only by
chance. The lower the E-value, the more
similar the sequences. If the E-value is less
than 1 X 10 -50 ,the hit is very similar to the
query sequence and is very likely to be
evolutionarily related.

GenBank
1. Locus gives us the locus name
2. Definition provides a short definition of the
gene
3. Accession lists the accession number, a unique
identifier within and across various databases.
4. Source divulges the common name of the
relevant organism to which the sequence
belongs
5. Organism gives a more complete identification
of the organism, complete with its technical
(!!!) taxonomic classification
6. Reference introduces a section ehere the
credits for the sequence determination are
given
7. Features describe precisely the gene regions
and the associated biological properties
Select FASTA in Display window!

GenBank
Select sequence, copy and paste
in a new text file. Create a file
with several sequences including
an outgroup taxa sequence.

TreeBase
TreeBASE is a relational database designed to manage and explore information on
phylogenetic relationships. Its main function is to store published phylogenetic trees and
data matrices. It also includes bibliographic information on phylogenetic studies, and some
details on taxa, characters, algorithms used, and analyses performed. The database is
designed to allow retrieval and recombination of trees and data from different studies,
and it can be explored interactively using trees included in the database. TreeBASE
therefore provides a means of assessing and synthesizing phylogenetic knowledge
http://www.treebase.org/treebase/

Useful databases for nematologists
WormBase (http://www.wormbase.org) is the central data
repository for information about Caenorhabditis elegans and related
nematodes. As a model organism database, WormBase extends
beyond the genomic sequence, integrating experimental results
with extensively annotated view of genome. WormBase also
provides large array of research and analysis tools.
NemaGene (http://www.nematode.net) is a web-accessible
resource for investigating gene sequences from nematode
genomes. The database is an outgrowth of the parasitic nematode
EST project. ESTs (Expressed Sequence Tag) are usually shorter
than the full-length mRNAs from which they are derived and are
prone to sequencing errors. The database provides EST cluster
consensus sequence, enhanced online BLAST search tools and
functional classification of cluster sequences.

Useful databases for nematologists
NEMBASE (http://www.nematodes.org) is a database providing
access to the sequence and associated meta-data currently being
generated as part of the parasitic nematode EST project. Users
may query the database on the basis of BLAST annotation,
sequence similarity or expression profiles. NEMBASE also features
an interactive which allows the simultaneous display and analysis of
the relative similarity relationships of groups of sequences to others
databases.
NemAToL (http://nematol.unh.edu) is an open database
dedicated to collecting, archiving and organizing video images
other morphological information, DNA sequences, alignments, and
other reference materials for study of the phylogeny and diversity,
and taxonomy, systematics, and ecology of nematodes.