ASSIGNMENT OF

BIOINFORMATICS LAB

SUBMITTED TO:
MS.NISHTHA PANDEY

SUBMITTED BY:
GAGANJIT KAUR
SECTION: A77E2
ROLL NO:27
ORF FINDER
QUES: What is ORF?
ANS: Open reading frame (ORF) is a DNA sequence that contains a start codon and a stop codon in
the same reading frame. In a gene, ORFs are located between the start-code sequence (initiation codon)
and the stop-code sequence (termination codon).

For example, if a portion of a genome has been sequenced (e.g. 5'-UCUAAAAUGGGUGAC-3'), and it is
known to contain a gene, ORFs can be located by examining each of the three possible ORFs (or six in
double-stranded DNA). In this sequence two out of three possible reading frames are "open". This is one
of the two possible mRNA sequences of the transcript, and we see that it can be read in three different
ways:

1. UCU AAA AUG GGU GAC

2. ..CUA AAA UGG GUG AC
3. ....UAA AAU GGG UGA C

The last reading frame contains a stop codon (UAA), unlike the first two. Thus, only two of the three
reading frames are open. Since there is a start codon (AUG) in the first open reading frame, it is very
likely that the first ORF is the correct one.

QUES: What is ORF finder?

ANS: The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading
frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino
acid sequence can be saved in various formats and searched against the sequence database using the WWW
BLAST server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions.
It is also packaged with the Sequin sequence submission software.
Steps involved in finding ORF:

STEP: 1 Go to in NCBI and put the name of the protein

(collagen) and select database nucleotide .click on search.
Results of collagen are founded.
STEP: 2 Click on one entry and and copy its accession
number or GI number.

STEP: 3 Paste this accession number or GI in orf finder.

STEP: 4 Click on orf find and see the results.
The +3, +2,+1 are the forward open reading frames and -1,-2,-3 are the backward
open reading frames. The color shows the length of the orf finder. +3 orf has
maximum length.

STEP: 5 Click on the +3 orf frame.

STEP: 6 Click on ACCEPT.
DOTTUP:
A dot plot is a graphical representation of the regions of similarity between two sequences.

The two sequences are placed on the axes of a rectangular image and (in the simplest forms of
dot plot) wherever there is a similarity between the sequences a dot is placed on the image.

Where the two sequences have substantial regions of similarity, many dots align to form
diagonal lines. It is therefore possible to see at a glance where there are local regions of
similarity as these will have long diagonal lines. It is also easy to see other features such as
repeats (which form parallel diagonal lines), and insertions or deletions (which form breaks or
discontinuities in the diagonal lines).

Dottup looks for places where words (tuples) of a specified length have an exact match in both
sequences and draws a diagonal line over the position of these words. This is a fast, but not
especially sensitive way of creating dotplots. It is an acceptable method for displaying regions of
substantial similarity between two sequences.

Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is less
sensitive. Shorter word sizes are more sensitive to shorter or fragmentary regions of similarity,
but also display more random points of similarity (noise) and runs slower.

STEP: 1Type any sequence in the empty square .And

select the word size 4 it means we compare four
nucleotide of one sequence with the other sequence. Now
click on the Run Dottup.
STEP: 2 Now see the results.
The lines show the matching part of sequence 1 with the sequence 2. By plotting
graph we can get regions of similarity between two sequences

BLASTp: Basic Local Alignment Search Tool, or BLAST, is an algorithm for

comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences.

BLASTP programs search protein databases using a protein query.

STEP: 1 Open swissprot and enter name of protein collagen and click on
search and see the results.
STEP: 2 Click on accession number of one entry and open its sequence in
FASTA format.
STEP:3 Open BLASTp.

STEP: 4Copy the sequence and paste in query box in

BLASTp and click on BLAST.
STEP: 5 See the results.
This shows the local alignment (not end to end alignment but determine similar
regions between two nucleotide or protein sequences instead of looking at the total
sequence).

STEP: 6 Click on one colored line and see the results.

In this there are two sequences one is query and the other is subject. The centered
sequence shows the similarity between the two sequences. The letters written in
the centered line are known as identities and positive sign shows the similarity in
physical properties in both the sequences such as both are hydrophobic in nature.
Gap shows there is no similarity between the two sequences.

o similarity between the two sequences.