This document provides information about different types of BLAST programs including BLASTN and TBLASTN. It discusses how BLASTN performs nucleotide sequence comparisons and TBLASTN translates nucleotide databases to protein sequences. The document also provides examples of running BLASTN and TBLASTN searches and analyzing the results, with screenshots of the outputs.

1. Name: Ayush Meshram
Sem: 1st
Subject:INTRODUCTIONTO BIOINFORMATICS&
SEQUENCE ANALYSIS
Guided by: Jerry ma’am
Date: 10-09-2022
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2. TBLASTN
Conclusion
BLASTN
Application
BLASTN TBLASTN Application Saturn
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3. TYPES OF BLAST
NATURE PROGRAM QUERY DATABASE
Nucleotide
BLAST
Blastn Nucleotide
(DNA/RNA)
Nucleotide
(DNA/RNA)
Protein BLAST Blastp Protein Protein
Blastx Translated
Nucleotide
Protein
Mixed BLAST tBlastn Protein Translated
Nucleotide
tBlastx Translated
Nucleotide
Translated
Nucleotide
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4. NBLAST
1
Standard Nucleotide BLAST
• BLASTN - The query is a nucleotide sequence -
The database is a nucleotide database - No
conversion is done on the query or database.
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5. INTRODUCTION
• The BLAST algorithm compares biological sequences
to one another in order to determine shared motifs
and common ancestry. However, the comparison of all
non-redundant (NR) sequences against all other NR
sequences is a computationally intensive task.
• We developed NBLAST as a cluster computer
implementation of the BLAST family of sequence
comparison programs for the purpose of generating
pre-computed BLAST alignments and neighbour lists
of NR sequences.
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6. NBLAST performs the heuristic BLAST algorithm and generates
an exhaustive database of alignments, but it only computes
alignments (i.e. the upper triangle) of a possible N2 alignments,
where N is the set of all sequences to be compared. A task-
partitioning algorithm allows for cluster computing across all
cluster nodes and the NBLAST master process produces a
BLAST sequence alignment database and a list of sequence
neighbours for each sequence record. The resulting
sequence alignment and neighbour databases are used to
serve the SeqHound query system through a C/C++ and
PERL Application Programming Interface (API).
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8. FASTA
Sequence
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9. Paste
FASTA Seq
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10. Result of
BLASTN
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11. Descriptions
of BLASTN
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12. Graphical
Summary of
BLASTN
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13. Alignments of
BLASTN
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14. Taxonomy
from BLASTN
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15. ANALYSIS
Fragmentation
chop query into
short words
Processing
Find exact
matches in the
database
Scoring
extend matches
and assign a
score
Result
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16. —BLASTN Applications
BLASTN application :The blastn application searches a nucleotide
query against nucleotide subject sequences or a nucleotide
database. An option of type “flag” takes no arguments, but if present
the argument is true. Four different tasks are supported:
1.) “megablast”, for very similar sequences (e.g, sequencing errors),
2.) “dc-megablast”, typically used for inter-species comparisons,
3.) “blastn”, the traditional program used for inter-species
comparisons,
4.) “blastn-short”, optimized for sequences less than 30 nucleotides.
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17. 2
Translated BLAST:
TBLASTN is a mode of operation for
BLAST that aligns protein
sequences to a nucleotide database
translated in all six frames.
tBLASTn
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18. tBLASTn
• We present the first description of the modern implementation
of TBLASTN, focusing on new techniques that were used to
implement composition-based statistics for translated
nucleotide searches.
• Composition-based statistics use the composition of the
sequences being aligned to generate more accurate E-values,
which allows for a more accurate distinction between true and
false matches.
• Until recently, composition-based statistics were available only
for protein-protein searches. They are now available as a
command line option for recent versions of TBLASTN and as an
option for TBLASTN on the NCBI BLAST web server.
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19. VERSIONS of TBLASTN
B-TBLASTN
This provides baseline behavior;
it ignores the composition of the
sequences and merely scales the
BLOSUM62 matrix to have five
more bits of accuracy before
rounding
S-TBLASTN
performs compositional
scaling
C-TBLASTN
erforms compositional
matrix adjustment
conditionally
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20. Comparison
• Statistical accuracy of
three variants of TBLASTN.
One thousand queries were
randomly selected from
mouse proteins, permuted,
and aligned to human
nuclear DNA.
• P = 1 - e -E
• A P-value represents the
probability that an
alignment of equal or
greater quality will be found
when the query and
database sequences are
unrelated.
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21. FASTA
Sequence
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22. Paste
FASTA Seq
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23. Result of
TBLASTN
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24. Descriptions of
TBLASTN
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25. Graphical
Summary of
TBLASTN
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26. Alignments of
TBLASTN
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27. Taxonomy
from
TBLASTN
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28. 1. BMC Biology:
https://bmcbiol.biomedcentral.com/articl
es/10.1186/1741-7007-4-41#Sec8
2. NCBI:
https://www.ncbi.nlm.nih.gov/books/NBK
1734/ .
3. Future Learn:
https://www.futurelearn.com/info/course
s/bacterial-genomes-
bioinformatics/0/steps/47023#:~:text=Fi
gure%201%20%E2%80%93%20The%20th
ree%20steps,matches%20and%20assign
%20a%20score%27
References:
THANKS
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