Ppt tblast bioinformatics

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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