assignment of tics lab

8/8/2019 Assignment of tics Lab

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ASSIGNMENT OF

BIOINFORMATICS LAB

SUBMITTED TO:

MS.NISHTHA PANDEY

SUBMITTED BY:

GAGANJIT KAUR

SECTION: A77E2ROLL NO:27


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ORF FINDER

QUES: Whatis 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.
http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Initiation_codonhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Initiation_codon


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Steps involved in finding ORF:

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

(collagen) and select database nucleotide .click on search.

Results of collagen are founded.


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STEP: 2Click on one entry and and copy its accession

number or GI number.

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


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STEP: 4Click on orf find and see the results.


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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: 5Click on the +3 orf frame.


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STEP: 6 Click on ACCEPT.


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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 ofdot 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 ofsimilarity 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 bothsequences 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 ofsubstantial similarity between two sequences.

Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is lesssensitive. 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. Nowclick on the Run Dottup.


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STEP: 2 Now see the results.


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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 forcomparing primary biological sequence information, such as the amino-acid

sequences of different proteins or the nucleotides ofDNA 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.
http://en.wikipedia.org/wiki/Algorithmhttp://en.wikipedia.org/wiki/Primary_structurehttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Algorithmhttp://en.wikipedia.org/wiki/Primary_structurehttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/DNA_sequence


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STEP: 2 Click on accession number of one entry and open its sequence in

FASTA format.


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STEP:3 Open BLASTp.

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

BLASTp and click on BLAST.


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STEP: 5 See the results.


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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.
http://en.wikipedia.org/wiki/Nucleotide_sequencehttp://en.wikipedia.org/wiki/Protein_sequencehttp://en.wikipedia.org/wiki/Nucleotide_sequencehttp://en.wikipedia.org/wiki/Protein_sequence

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