Tema 13. Sequence comparison. Concept of homology. Sequence alignment. Comparison strategies. BLAST, PSI-Blast. Multiple alignment, profiles. Families of proteins. Functional prediction based on sequence. Gabriel Pons, Departament de Ciències Fisiològiques II, Campus de Ciències de la salut. Bellvitge. Universitat de Barcelona
41
Embed
Tema 13. Sequence comparison. Concept of homology. Sequence alignment. Comparison strategies. BLAST, PSI-Blast. Multiple alignment, profiles. Families.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Tema 13. Sequence comparison. Concept of homology. Sequence alignment. Comparison
strategies. BLAST, PSI-Blast. Multiple alignment, profiles. Families of proteins.
Functional prediction based on sequence.
Gabriel Pons, Departament de Ciències Fisiològiques II, Campus deCiències de la salut. Bellvitge. Universitat de Barcelona
Sequence comparison
Goals
• To take advantage from functional or structural information identifiyng homologies between sequences
• Differences between Homology and identity
• Two sequences are homologous when:– They have the same evolutive origin– They have similar function and structure
• Homologous sequences - sequences that share a commonevolutionary ancestry• Similar sequences - sequences that have a high percentage ofaligned residues with similar physicochemical properties(e.g., size, hydrophobicity, charge)
IMPORTANT:• Sequence homology:• An inference about a common ancestral relationship, drawn whentwo sequences share a high enough degree of sequence similarity• Homology is qualitative• Sequence similarity:• The direct result of observation from a sequence alignment• Similarity is quantitative; can be described using percentages
More definitions
• Orthologs: sequences which exactely correspond to the same function/structure in different species
• Paralogs: sequences produced by gene duplications in the same organism. Usually, it involves change in function, but keeping functional relationship many times.
Homology
Homology and prediction
• Very divergent protein sequences may suport similar structures
• Similar protein structures will probably have related or similar functions
3D STRUCTURE VERSUS SEQUENCESequence alignment between human myoglobin, and globins from hemoglobin
myoglobin -globin -globin
Comparison of 3D structures of human myoglobin, and globins from hemoglobin
Superposition of 3D structures of human myoglobin and globin from hemoglobin
Homology and prediction
• Sequence comparison is the simplest method in order to identify the presence of homology between sequences.
• Identity > 30% in proteins involves homology (>65% nucleic)
• Identity > 80-90% usual in orthologs from close species
• Identity 10-30%. If there is homology may be not detectable (“twilight zone”)
No me gusta la bioinformaticaTeme usted la ionosfera optica
• Global alignment– Finds best possible alignment across entire length of 2
sequences– Aligned sequences assumed to be generally similar over entire
length• Local alignment
– Finds local regions with highest similarity between 2 sequences– Aligns these without regard for rest of sequence– Sequences are not assumed to be similar over entire length
Comparación de secuencias contra bases de datos
Secuencia incógnitaATTVG...LMN
Base de datos De secuencias
AGLM...WTKRTCGGLMN..HICGWRKCPGL...
Requiere algoritmos de comparación muy rápidos
Alignments
• “pairwise”– 2 sequences
• Multiple– More than 2 sequences
• Global– Whole sequence is considered
• Local– Only similar regions are aligned
Diasdvantages from global alignment
• Slow
• Scores whole sequence– Do not recognize multidomain proteins
• E value:• Expect: This setting specifies the statistical significance threshold for reporting
matches against database sequences. The default value (10) means that 10 such matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported.
E = K.m.n.e-.S
• Warning:
• E → Falsos negativos
Score
Normalization factors
Number of letters in query
Number of letters in data baseScore
E parameter (More)• Expect
For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance. This means that the lower the E-value, or the closer it is to "0" the more "significant" the match is. However, keep in mind that searches with short sequences, can be virtually indentical and have relatively high EValue. This is because the calculation of the E-value also takes into account the length of the Query sequence. This is because shorter sequences have a high probability of occuring in the database purely by chance.