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Showing posts with label bioinformatics. Show all posts
Showing posts with label bioinformatics. Show all posts
Thursday, August 19, 2010
Bioinformatics Web Practical
4:39 AM
GCbioinfo
It is an online practical for the prediction of the structure and function of the unknown protein by using primary and secondary biological databases
First go http://umber.embnet.org/dbbrowser/bioactivity/
press "ready to go" and then "go" now you are at the page http://umber.embnet.org/dbbrowser/bioactivity/nucleicfrm.html at the top of the you have Sequence translation & identification select "materials" which contain the unknown nucleotide sequences you can also use your own sequence of interest click materials and select any fragment it is the dna sequence click the fragment and get its sequence copy this sequence and paste it in translator to get the translated sequence and also find the orf(open reading frame) of the sequence . Copy the orf and paste in OWL which is actually contain information to which organism your query sequence is present. Find the exact match of your sequence.After finding the exact match copy the name of the organism and paste in query at http://umber.embnet.org/dbbrowser/bioactivity/proteinfrm.html to get the full protein sequence to which our query is part.After getting the full sequence copy it and paste in psi blast to get similarity to other related proteins
now you can find the structure and function of the protein by using this primary database the secondary database procedure will be told you latter. The first hit of the blast result will be the sequence of our query protein you can find its structure and function and compare its structure and function to other hits.
First go http://umber.embnet.org/dbbrowser/bioactivity/
press "ready to go" and then "go" now you are at the page http://umber.embnet.org/dbbrowser/bioactivity/nucleicfrm.html at the top of the you have Sequence translation & identification select "materials" which contain the unknown nucleotide sequences you can also use your own sequence of interest click materials and select any fragment it is the dna sequence click the fragment and get its sequence copy this sequence and paste it in translator to get the translated sequence and also find the orf(open reading frame) of the sequence . Copy the orf and paste in OWL which is actually contain information to which organism your query sequence is present. Find the exact match of your sequence.After finding the exact match copy the name of the organism and paste in query at http://umber.embnet.org/dbbrowser/bioactivity/proteinfrm.html to get the full protein sequence to which our query is part.After getting the full sequence copy it and paste in psi blast to get similarity to other related proteins
now you can find the structure and function of the protein by using this primary database the secondary database procedure will be told you latter. The first hit of the blast result will be the sequence of our query protein you can find its structure and function and compare its structure and function to other hits.
Tuesday, August 17, 2010
Databases used in Bioinformatics
7:58 AM
GCbioinfo
The Databases (and their acronyms!):
Genbank, operated by NCBI (National Center for Biotechnology Information)
Contains all publicly available sequences of DNA, with annotations
Same DNA sequence content as EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Data Bank of Japan)
Swiss-Prot and TrEMBL, operated by SIB (Swiss Institute of Bioinformatics) and EBI (European Bioinformatics Institute)
Contains most of the publicly available sequences of proteins, with annotations
Protein Data Bank
Contains all publicly availalble experimentally determined structural models of proteins and nucleic acids (determined by x-ray crystallography and NMR)
Swiss-Model Repository
Contains many theoretical structural models of proteins (determined by automated homology modeling)
Online Mendelian Inheritance in Man
A catalog of human genes and genetic disorders, linked to gene entries in GenBank
Genbank, operated by NCBI (National Center for Biotechnology Information)
Contains all publicly available sequences of DNA, with annotations
Same DNA sequence content as EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Data Bank of Japan)
Swiss-Prot and TrEMBL, operated by SIB (Swiss Institute of Bioinformatics) and EBI (European Bioinformatics Institute)
Contains most of the publicly available sequences of proteins, with annotations
Protein Data Bank
Contains all publicly availalble experimentally determined structural models of proteins and nucleic acids (determined by x-ray crystallography and NMR)
Swiss-Model Repository
Contains many theoretical structural models of proteins (determined by automated homology modeling)
Online Mendelian Inheritance in Man
A catalog of human genes and genetic disorders, linked to gene entries in GenBank
