How to use databases

Submitted by:

Menahel Bint-e-Khalid

Submitted to:

Sir Omar Khan

Course Code :

BNB-405

Course title:

Bioinformatics

BS(3rd)Bacholer of Eastern Medicine and Surgery

Govt. College University Faisalabad

NCBI
The National Center for Biotechnology Information advances science and health by
providing access to biomedical and genomic information. Following are the steps to use
NCBI.

Step 1:

 First search for NCBI in browser.

 e.g.,chrome , google

Step 2:

 Open the first link “national centre for biotechnology information”.

 The link opens to following website.

Step 3:
  To limitalize the search open the option “all databases” from the upper right corner and
select the option according to your search, as I wanna search about nucleotide i select
the option “nucleotide” from the given options.

Step 4:

 Now add name of desired protein in the search bar.

 such as “glial fibrillary acidic protein” and search for it.

 Following page will open, which show the sequences of all organisms.
Step 5:

 Now if you want only the sequence of one organism, limitalize the search by selecting
one organism from the upper left corner
 I limitalize the search to “ Homo Sapien”

 Then the results shown will only be related to “Homo Sapien”

 Select the complete coding sequence (cds) of the desired protein.

Step 6:

 the sequence will open in “Gen Bank” format

 which shows the following characters,
 LOCUS : HUMGFAP 3017 bp mRNA linear PRI 08-NOV-1994
 DEFINITION: Human glial fibrillary acidic protein (GFAP) mRNA, complete cds.
 ACCESSION no: J04569
 VERSION : J04569.1
 KEYWORDS: glial fibrillary acidic protein.
 SOURCE : Homo sapiens (human)
 ORGANISM : Homo sapiens
 and also many more features
 We can also open the sequence in “FASTA” format by selecting FASTA from the upper
right corner.

 and can also make a file of the sequence in “FASTA” format by clicking “send to” from
the upper left corner and choose the option “file” and then select the desired file
format such as “FASTA” and then select option “create file” the file will created and
downloaded in “FASTA” format.

 the other way to make “FASTA” file is to copy the sequence in FASTA format and then
paste it in “MS Word” and give a name to the file and then save it.
 The other feature is that you can also see the “graphics” of the sequence by clicking
graphics from the upper right corner.

 NCBI supports many other functions like it also gives “related information” about the
sequence by different authors such as “PubMed”, which contains more than 36 million
citations and abstracts of biomedical literature.
 Select the PubMed from the lower left corner in related information.

 From the lower left corner you can also see your recent activity.
 Cell Biol

Cell biol is a database which is used to clean any sequence by removing the meaningless
information. Following are the steps to use cell biol sequence cleaner.

Step 1:

 Search for “Cell Biol sequence cleaner” in any browser.

 e.g.,chrome , google

Step 2:

 Open the first link “DNA protein sequence cleaner”.

 The link opens to following website.

.
Step 3:

 Scroll down the page and following features will shown.

Step 4:

 In order to clean a sequence, first copy the sequence to whom you wanna clean.
 I copied the sequence of “glial fibrillary acidic protein” from FASTA format.

Step 5:

 Now paste the sequence in cell biol sequence cleaner and click “clean it”.
  Now it will show the cleaned sequence.

EBI Translate Tool

EBI Translate tool allows the translation of a nucleotide (DNA/RNA) sequence to a

protein sequence. Following are the steps to use EBI translate tool.

Step 1:

 First Search for “EBI Translate tool” in any browser.

 e.g.,chrome , google
Step 2:

 Open the first link “EMBOSS Transeq -Sequence Translation”

 The link opens to following website

 Scroll down the page and following features will shown.

Step 4:

 In order to translate the DNA sequence into protein, copy the sequence which you want
to translate.
 I copied the sequence of “glial fibrillary acidic protein” from FASTA format.
  And then paste it in the translate tool.

Step 5:

 Now scroll down and select parameters according to your demand and then submit it.
 If you wanna notified on your email you can tick the box above to submit button.

Step 6:

 After submitting , the sequence will be translated into protein.

 You can also see the results in colors.
 You can also download it .
 And can also see its submission details.


 BLAST

Basic Local Alignment Search Tool finds regions of similarity between biological
sequences. The program compares nucleotide or protein sequences to sequence
databases and calculates the statistical significance.

Step 1:
 First Search for “BLAST” in any browser.
 e.g.,chrome , google

Step 2:
 open the first link “BLAST: Basic Local Alignment Tool”.

 the link opens to following page.

Step 3:
 Scroll down the page and following features will shown.
 Select the first web blast “nucleotide BLAST”.

 Following page will open.

 Which show the blank box where the query sequence has to be paste.
 Or either search by accession number, also by pasting FASTA sequence and by
uploading file.

 I Copy the sequence whom for i wanna find similarity.

 and paste the sequence in the blank space.

Step 4:
 Now give your job a name.
 I given the name “glial fibrillary acidic protein”
 Next to choose the “search set” by selecting “database at standard form”.
  You can also choose the organism.

Step 5:
 Now select the program to “highly similar sequences (megablast)”.
 And then click on BLAST and BLAST the sequence.

 the results will show the similarity of the searched sequence with the given
following sequences.
 Clustal Omega
It is a new multiple sequence alignment program that uses seeded
guide trees and HMM profile-profile techniques to generate alignments
between three or more sequences. It can also be used for pairwise
sequence alignment.

Step 1:

 First Search for “clustal omega” in any browser.

 e.g.,chrome , google

Step 2:

 open the first link “Clustal Omega-Multiple Sequence Alignment”.

 the link opens to following page.

Step 3:

 Scroll down the page and following features will shown.

 I Set the first field to DNA.
 Then I copy the two sequences give them names and paste them in the 2 nd field.

Step 4:

 More scroll the page and set the parameters according to your demand.

 And scroll down and submit your job.

 If you wanna notified on your email you can tick the box above to submit button.
Step 5:

 The results will show the alignment of the two sequences.

 Steric * sign will show the similarity between the sequences.
 and hyphen- sign will show the gaps or mismatched parts.
 Now there also many options like you can see the result summary, result viewers,
submission details and can also download the alignment file.

Step 6:

 You can also see the phylogenetic tree of both sequences.

 Which show the divergence or resemblense of organism to ancestor.
 Or in other words, how far the organism evoluate from ancestor.