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BIOINFORMATICS
TOOLS
| Biological
Data Retrival Tools |
Entrez
Entrez is a search
and retrieval system developed by the NCBI ,which contains an
integrated view of portions of MEDLINE, and all publically available
nucleotide and protein databases, including GenBank.
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SRS
SRS had been developed
at the EBI. SRS system similar to Enterz that provides search
facilities for a large number of databases, and provides links
between them.
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| Translation
of DNA to protein sequence |
TRANSLATE
TOOL :
A tool which allows
the translation of a nucleotide (DNA/RNA) sequence to a protein
sequence. - by ExPASy
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EMBOSS
Transeq :
Translates nucleic
acid sequences to the corresponding peptide sequence. It can translate
in any of the three forward or three reverse sense frames, or
in all three forward or reverse frames, or in all six frames.
- by EMBL-EBI.
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| Pairwise
Sequence Alignment Tools: |
Emboss
Pairwise Alignment Tool
This tool is used
to compare 2 sequences.you can perform either local or global
sequence alignment between two protein or nucleic acid sequences.
Most important application of pairwise alignment
methods is for identifying sequences of unknown structure/function.
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LALIGN
This tool is used
to find multiple matching sub-segments in two sequences available
at the Swiss Institute for bioinformatics.
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| Multiple
Sequence AlignmentTools |
ClustalW
ClustalW is popular
software for multiple sequence alignment. It can be used on either
DNA or proteins. The output of ClustalW is a multiple alignment,
shown graphically, and it also produces phylogenetic trees according
to the alignment which is useful to view the evolutionary relationships
.
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TCoffee
A novel method for
multiple sequence alignments, produces better mulitple alignments
than clustalw in very pleasing colours.
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| Similarity
search and sequence alignment |
NCBI
BLAST:
Blast is standard
tool for sequence analysis, that enables a researcher to
look for sequences that either duplicate or resemble any sequence
of interest.
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SIB
BLAST:
This NCBI BLAST2 service
is maintained by the Swiss Institute of Bioinformatics.
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ScanProsite:
A program allows to
scan a protein sequence (either from SWISS-PROT or TrEMBL or provided
by the user) for the occurrence of patterns and profiles stored
in the PROSITE database, or to search protein databases with a
user-entered pattern. - by ExPASy.
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Motif
Scan:
Motif scanning means
finding all known motifs that occur in a sequence. - by SIB
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Pfam:
Protein families database
of alignments and HMMs. - by Sanger Institute, UK .
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SMART
:
A Simple Modular Architecture
Research Tool that allows the identification and annotation of
genetically mobile domains and the analysis of domain architectures.
- by EMBL .
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InterProScan:
InterProScan
is one of the tools used for searching protein function based
on integrated search - by EBI .
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Phylip
A program allows to
scan a protein sequence (either from SWISS-PROT or TrEMBL or provided
by the user) for the occurrence of patterns and profiles stored
in the PROSITE database, or to search protein databases with a
user-entered pattern. - by ExPASy.
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MEGA
Motif scanning means
finding all known motifs that occur in a sequence. - by SIB
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| Molecule
Structure Visualization Tools |
RasMol
RasMol is a very popular
program . It allows users to move, zoom, rotate, or change display
colors so that the best image or viewpoint can be obtained.
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Cn3D
Cn3D is a helper
application for your web browser that allows you to view 3-dimensional
structures from NCBI's Entrez retrieval service. Cn3D allows users
to correlate structure and sequence information. To better understand
on Cn3D Take a look at Cn3D
Tutorial at NCBI
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| For
more information use the following links |
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