BIF501 Assignment 1 Solution by Arham

BIOINFORMATICS-II · ASSIGNMENT NO. 1 · SEMESTER SPRING 2022 · MS. KHIZRA MAQSOOD · SUMITTED TO: · BIF501

Describe Five DNA Sequence Formats By Giving Examples Write Methods For Retrieving DNA Data From NCBI

SUBMITTED BY: · ARHAM · DUE DATE: 20 JUNE 2022 · DINNING DISCUSSION · Virtual University Of Pakistan · Assignment Questions · 1. Describe Five DNA Sequence Formats By Giving Examples · 2. Write Methods For Retrieving DNA Data From NCBI · 3. Describe Three DNA Databases · Solution · 1. Describe Five DNA Sequence Formats By Giving Examples

I.

FASTA Format

In bioinformatics, FASTA format is a text-based format for representing DNA sequences, in which base pairs are represented using a single-letter code [A,C,G,T,N] where A=Adenosine, C=Cytosine, G=Guanine, T=Thymidine and N= any of A,C,G,T. The format also allows for sequence names and comments to precede the sequences. A sequence in FASTA format begins with a single-line identifier description, followed by lines of DNA sequence data. The identifier description line is distinguished from the sequence data by a greaterthan ('>') symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is a description (optional) separated form the identifier by a white space or tab. The sequence data starts on the next line following the text line and ends if another line starting with a ">" appears; this indicates the start of another sequence.

Examples of the FASTA format:

>P01013 GENE X PROTEIN (OVALBUMIN-RELATED) QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVAT LPAE KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKY NLTS VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFR ADHP FLFLIKHNPTNTIVYFGRYWSP

II. GeneBank Sequence Format

GeneBank sequence format is found to be in the GeneBank Database which is a kind of standard format and other formats are pretty similar to it. GenBank format (GenBank Flat File Format) stores sequence and its annotation together. The start of the annotation section is marked by a line beginning with the word “LOCUS”. The start of sequence section is marked by a line beginning with the word “ORIGIN” and the end of the section is marked by a line with only “//”.

Example of the GeneBank Sequence Format:

LOCUS AB000263 368 bp mRNA linear PRI 05-FEB-1999 DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.

ACCESSION AB000263 · ORIGIN · 361 gacctgaa

III.

EMBL Format

EMBL format stores sequence and its annotation together. The start of the annotation section is marked by a line beginning with the word “ID”. The start of sequence section is marked by a line beginning with the word “SQ”. The “//” (terminator) line also contains no data or comments and designates the end of an entry.

Example of the EMBL Format : · XX · AC AB000263; · XX · XX