Comprehensive Insights into EBI and Essential Bioinformatics Tools

so apart from this apart from all these European databases that we discussed there's one more you know remember I

told you earlier that one such example is ebi ebi European bioinformatics

Institute and this name is you know something like very very important in terms of bioinformatics tools two name

ebi and ncbi ebi is European bioinformatics Institute and ncbi is National Center of biotechnology

information both are playing The crucial role in maintaining a huge amount of data in all the different kinds of

database so European biological or European bioinformatics Institute under uh it is under

embl okay what is embl full form European molecular biology laboratory embl they provide the bioinformatics

information it's actually very important that we have a lab facility which is wet lab facility of course and then we have

this dry lab facility so what is the difference between the weight lab and dry lab and cross flow let's understand

we have weight lab where we run all the experiment experiments are done experiments on uh on DNA RNA uh

experiments on protein all these things we perform we do and then all the data that we gather is transferred to the dry

lab where we store the data we analyze the data we modify the data and we cross

talk or cross check cross check sorry cross check after after what cross check after modification after

uh prediction so we do prediction here of course we do prediction and then you cross check that prediction and then

based on that we get a yes or no or nod up or no based on that we can understand an organism and how that

organism behaves because now basically it's not likely you know there are plenty of years earlier when we see an

organism based on its morphology appearance we decide everything but nowadays we don't even look at

morphology it doesn't matter whether how much similar they look from outside phenotype doesn't matter everything that

matter is the genotype how it's actually made up and everything is possible with this cross stock of weight lab and dry

lab so that's why this always the greatest uh biotechnology greatest bioinformatics tools can only be

hosted when they are connected to molecular lab or weight lab facility so for example here is the European

molecular biology laboratory embl under this we run the experiment on all and that hosts in the ebi okay it was

established in 1980s okay at embl okay and it was first as a nucleotide sequence database it

started as a nucleotide sequence database and then sooner it man start managing different kinds of biological

databases and now what we have we have DNA sequences genome sequences we have microarrays proteomics structural

genomics and so many different different things are under this roof and basically when you heard this name you know

genomics proteomics structural genomics all this sounds very complicated all these sounds very you know similar so

people use these terms quite often so for that also I'll do a midv portion at the end of this lecture which will help

you to understand and forget all the misconception and understand only what is real

okay so always we have a we need a need we require a need to collect store and curate all the little bit of information

from genome proteome uh structure of the protein and all the different places and put them together okay and we have

multiple genome projects running uh in different places of the earth okay and the data came in so we'll gather them

okay so what happened in 1992 embl voted to establish this ebi and then the ebi got established embl

started then and the ebl got established 1992 okay so basically it provides the search assisted to lead B

informatic Revolution that is what ebi is actually made for and now ebi hosts various

databases various it actually let me write it hosts various various

databases okay so this various database what kind of database it can be it can be nucleotide database right it can be

microarray microarray database it can be Pathways protein Pathways okay there are different

Pathways available that database uh protein structural datab all these different types of database

hosted under this ebi and there are various tools available as well there are various tools available that

actually there various tools that will help us to find out information regarding all these different type from

different type of database like nucleotide sequence microarray Pathways protein sequence and protein structure

okay so for example let me write down important name of the tool one of them is Pratt p r a t Pratt okay why Pratt is

formed to find patterns patterns basically conserved patterns

conserved patterns okay second thing PP search we have PP search

now why PP search is for basically it is there to compare the query sequence query

sequence me sequence that we feed in against all patterns that are stored in the proos site database that is called

PP search comparison okay okay another tool

inter Pro Scan inter Pro Scan what it

does basically we have inter Pro and the query sequence is scanned against the

interpro interpro has some information so we scan it against it then we have what else we have

emboss emboss all capital basically it's a sequence comparison tool sequence

quence comparison end to end comparison every little detail will be compared in emboss

what else we'll have pride p r i d all capital Pride what is

for proteomics proteum miix data okay what else we have let me write

another tool name align align what align stand for basically alignment what we do we do

pairwise Global and pairwise local alignment pairwise Global and local alignment is done with

alignment okay clustal W2 clustal W2 what it does again a tool for multiple sequence alignment multiple

sequence align MSA there are different types of alignments remember we'll discuss about that in lat separate

lecture multiple sequence alignment in clal W2 align is we'll do the global alignment and local

alignment what else we have saps what saps is for statistics of protein

sequence statistical tool statistics of protein sequence that is

saps what we have else we have faster faster what we do sequence

similarity searching tool is faster then what we have blast we have blast what is Blast for

again sequence similarity searching tool fasta blast both do the similar thing little difference we'll talk about that

later on what else we have number

11 Del light DL light what we do pairwise sequence or

pairwise actually pairwise structural comparison this is structural

comparison here you can see fasta and blast will do sequence similar it search while di light or Daily Light

will do structural comparison okay what else we

have read sequence this is known as sequence format conversion tool and it is very

very important actually right now you may not understand why it is important to convert a sequence there are

different formats of sequence just like there are different format of a file Know video file when you play uh there

is MP4 do Avi okay M 2m4 so we have different kinds as well in case of uh this sequence uh this this information

that we have that are available because we are doing this for different databases the datab there's ncbi there

are some database hosted by us their database hosted by UK they do this in different ways their own terms so the

the raw file have different formats so the format conversion is also important and read sequence will do the format

conversion format conversion okay there are some more

examples if you open up the site you'll see that but I'm not going to write them down here so these are all the types of

tools uh that are available there under ebi even there are four five more tools available tiof is also there

which is known for multiple sequence alignment okay uh then there is also pdb site pdbe site uh that helps us to

search active site based on liand where exactly it binds so let me write that one that's important pdb all capital pdb

E then site simply okay uh it helps helps us to find out uh active site active site

in enzyme based on liand or liand binding liand

binding okay so there are some more tools available out there you can check them out