# es/by-sa/2.0/. From Genes to Proteins (and a little bit about allignments) Prof:Rui Alves 973702406.

## Presentation on theme: "es/by-sa/2.0/. From Genes to Proteins (and a little bit about allignments) Prof:Rui Alves 973702406."— Presentation transcript:

http://creativecommons.org/licens es/by-sa/2.0/

From Genes to Proteins (and a little bit about allignments) Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/

(and a little about allignments) How does blast work?

How Does BLAST Really Work? The BLAST programs improved the overall speed of searches while retaining good sensitivity (important as databases continue to grow) by breaking the query and database sequences into fragments ("words"), and initially seeking matches between fragments.

BLAST Algorithm

How Does BLAST Really Work? Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S".

BLAST Algorithm

Extending the High Scoring Segment Pair (HSP) Neighborhood Score Threshold Minimum Score Significance Decay

BLAST Algorithm Sequences are split into words (default n=3) –Speed, computational efficiency Scoring of matches done using scoring matrices HSP = high scoring segment pair –BLAST algorithm extends the initial “seed” hit into an HSP Local optimal alignment More than one HSP can be found

Where does the score (S) come from? The quality of each pair-wise alignment is represented as a score and the scores are ranked. Scoring matrices are used to calculate the score of the alignment base by base (DNA) or amino acid by amino acid (protein). The alignment score will be the sum of the scores for each position.

Organization of the Talk From cDNA sequence to protein sequence.

Predicting protein sequence from DNA sequence Protein sequence can be predicted by translating the cDNA and using the genetic code.

Translating cDNA into protein sequence ATGTCTCTTATATGA… MetSerLeuIleTer No Gene!!!!!

Sometimes stop codons are not stop codons.

Are there alternative genetic codes? YES!!!!

CodonUniversal code AAAKN(9,14) AACK AAGN AATN ACAT ACCT ACGT ACTT AGAREND(2)S(5,9,14,21)G(13) AGCS AGGREND(2)S(5,9,14,21)G(13) AGTS ATAIM(2,3,5,13,21) ATCI ATGM ATTI Echinoderm/ Flatworm mitochondria Flatworm mitochondria Vertebrate mitochondria Yeast mitochondria Invertebrate mitochondria Ascidian mitochondria Trematode mitochondria

CodonUniversal code CAAQ CACH CAGQ CATH CCAP CCCP CCGP CCTP CGAR CGCR CGGR CGTR CTALT(3) CTCLT(3) CTGLT(3)S(12) CTTLT(3) Yeast mitochondria Candida

CodonUniversal code GAAE GACD GAGE GATD GCAA GCCA GCGA GCTA GGAG GGCG GGGG GGTG GTAV GTCV GTGV GTTV

CodonUniversal code TAAENDQ(6)Y(14) TACY TAGENDQ(6,15)L(16,21) TATY TCASEND(21) TCCS TCGS TCTS TGAENDW(2,3,4,5,6,9,13,14,21)C(10) TGCC TGGW TGTC TTAL TTCF TTGL TTTF Ciliate, Dasycladacean Hexamita

Translating yeast mitochondrial cDNA into protein sequence ATGTCTCTTATATGA………SECIS sequence TrpSerThrMetsCys MetSerLeuIleTer There is a Gene with a considerably different protein sequence from the one we would predict from the universal genetic code!!!!!

What changed? END→AA (16 events, all ter codons) AA →END (3 events) AA →AA’ (22 events, 3 AA)

Conclusions Translating DNA or mRNA sequence into proteins is easy but you need to be carefull as to which genetic code you need to use.