Fasta and genebank alignment

1. Assignment topic:FASTA and Genebank Alignment
HAFIZ M
WASEEM
UE
LAHOR
E

2. FASTA ALIGNMENT
 FASTA:
"In bioinformatics , FASTA is a text based format for representing
either nucleotide sequences or amino acid (protein) sequences, in which
nucleotides or amino acids are represented using single-letter codes."
PROCEDURE :
 Collect four different alpha globin fasta formats of species
namely,Cyprinus carpio ( common carp), Homo sapiens ( human) ,Mus
musculus ( house mouse) and Capra hircus ( goat) and place them in a
document.
 Search Clustal Omega on google .
 Enter input sequence as protein
 Paste the collected fasta formats from document .
 Select output format as Clustal W with character counts and press
the submit option .
 Result will be shown on screen.

10. INTERPRETATIONS:
In alignment section, multiple alignment sequences of four
different alpha globin show following four symbols:
* (Asterix) indicate positions with single fully conserved
sequence.
: (Colon) indicates conservation between amino acid groups
of strongly similar properties.
. ( Period) indicates positions with conservation between
amino acid groups of weekly similar properties.
- (Gaps) indicate one or more amino acid residues have been
deleted from the sequence.

11. CONTI...
Since Clustal Omega gives a multiple sequence alignment of amino acids and
nucleotides.FASTA formats of common carp, humans, house mouse and goat show
about eight sequence alignments.
Alignment # 1 : It contains 14 Asterisks 1 colon 7 Periods and 16 gaps.
Alignment# 2: It contains 22 Asterisks 4 colons and 9 periods.
Alignment# 3 : It contains 27 Asterisks 1 colon 9 periods and 9 gaps.
Alignment#4: It contains 21 Asterisks 2 colons and 11 periods.
Alignment#5: It contains 34 Asterisks 1 colon and 5 periods.
Alignment# 6 : It contains 30 Asterisks 3 colons and 5 periods .
Alignment# 7: It contains 22 Asterisks 1 colon 5 periods and 12gaps.
Alignment#8: It contains 10 Asterisks 1 colon 3 periods.

12. RESULTS:
 Total Asterisk = 180
Total Colon = 14
Total Period= 58
Total Gap = 37

13. RESUTS IN TABLE FORM

14. GENEBANK ALIGNMENT
 "The Genbank format allows for the storage of information in
addition to a DNA/protein sequence. It holds much more information
than the FASTA format".
PROCEDURE :
 Collect four different alpha globin genebank formats of species
namely,Cyprinus carpio ( common carp), Homo sapiens ( human)
,Mus musculus ( house mouse) and Capra hircus ( goat) and place
them in a document.
 Search Clustal Omega on google .
 Enter input sequence as DNA.
 Paste the collected genebank formats from document .
 Select output format as Clustal W with character counts and press
the submit option .
 Result will be shown on screen.

22. INTERPRETATION:
 Since Clustal Omega gives a multiple sequence alignment of
amino acids and nucleotides.Genebank formats of common carp,
humans, house mouse and goat show about eight sequence
alignments.Genebank formats show only two symbols ( Asterisk
and gap).
Alignment # 1 : It contains 18 Asterisks.
Alignment# 2: It contains 24 Asterisks.
Alignment# 3 : It contains 29 Asterisks and 9 gaps.
Alignment#4: It contains 19 Asterisks.
Alignment#5: It contains 38Asterisks.
Alignment# 6 : It contains 28 Asterisks.
Alignment# 7: It contains 20 Asterisks.
Alignment#8: It contains 9 Asterisks .

23. RESULTS:
Total Asterisk =185
Total Gap = 09

24. RESUTS IN TABLE FORM