Biology and computers
... Understand how the Smith-Waterman algorithm can be applied to perform local alignment. Have a general understanding about PAM and BLOSUM ...
... Understand how the Smith-Waterman algorithm can be applied to perform local alignment. Have a general understanding about PAM and BLOSUM ...
Introduction to bioinformatics
... Knowledge of protein structure facilitates drug design Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-up Genome analysis allows the targeting of genetic ...
... Knowledge of protein structure facilitates drug design Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-up Genome analysis allows the targeting of genetic ...
Compression of Gene Coding Sequences
... The gene coding sequences are believed to be the most informative part of the genome. These sequences are often stored as a sequence of letters, each representing a nucleotide and each three of which correspond to an amino acid. The genetic code has some redundancy. There are 43 possible codons but ...
... The gene coding sequences are believed to be the most informative part of the genome. These sequences are often stored as a sequence of letters, each representing a nucleotide and each three of which correspond to an amino acid. The genetic code has some redundancy. There are 43 possible codons but ...
BLAST etc.
... initn: 1565 init1: 1515 opt: 1687 Z-score: 1158.1 expect(): 2.3e-58 66.2% identity in 875 nt overlap ...
... initn: 1565 init1: 1515 opt: 1687 Z-score: 1158.1 expect(): 2.3e-58 66.2% identity in 875 nt overlap ...
Mining Single Nucleotide Polymorphisms from public sequence
... SNPs (single nucleotide polymorphisms) are abundant and useful genetic markers. Software exists to mine them from public data sets, but this doesn’t work in real time. GRID technology could help to deliver up-to-date alignments to users for any query sequence with putative SNPs marked up. Related us ...
... SNPs (single nucleotide polymorphisms) are abundant and useful genetic markers. Software exists to mine them from public data sets, but this doesn’t work in real time. GRID technology could help to deliver up-to-date alignments to users for any query sequence with putative SNPs marked up. Related us ...
Mining SNPs from public sequence Databases
... SNPs (single nucleotide polymorphisms) are abundant and useful genetic markers. Software exists to mine them from public data sets, but this doesn’t work in real time. GRID technology could help to deliver up-to-date alignments to users for any query sequence with putative SNPs marked up. Related us ...
... SNPs (single nucleotide polymorphisms) are abundant and useful genetic markers. Software exists to mine them from public data sets, but this doesn’t work in real time. GRID technology could help to deliver up-to-date alignments to users for any query sequence with putative SNPs marked up. Related us ...
BSC 219
... Due 10/18/12 1) ( 3 points) Describe the main ways that eukaryotic transcription initiation is different from prokaryotic transcription initiation. Eukaryotic initiation involves a large number of proteins to form an initiation complex that recruits RNA Polymerase to the promoter region. The DNA seq ...
... Due 10/18/12 1) ( 3 points) Describe the main ways that eukaryotic transcription initiation is different from prokaryotic transcription initiation. Eukaryotic initiation involves a large number of proteins to form an initiation complex that recruits RNA Polymerase to the promoter region. The DNA seq ...
BLAST seminar
... •The expect value E is the number of alignments with scores greater than or equal to the current score S that are expected to occur by chance in a database search. • e.g. an E value of 5 assigned to a hit indicates that in a database of the current size one might expect to see 5 matches with a simil ...
... •The expect value E is the number of alignments with scores greater than or equal to the current score S that are expected to occur by chance in a database search. • e.g. an E value of 5 assigned to a hit indicates that in a database of the current size one might expect to see 5 matches with a simil ...
tutorialdm
... Orthologs – Homologs produced by speciation. They tend to have similar function Paralogs – Homologs produced by gene duplication. They tend to have differing function Xenologs – Homologs resulting from horizontal gene transfer between two organism ...
... Orthologs – Homologs produced by speciation. They tend to have similar function Paralogs – Homologs produced by gene duplication. They tend to have differing function Xenologs – Homologs resulting from horizontal gene transfer between two organism ...
Document
... Global algorithms are often not effective for highly diverged sequences - do not reflect the biological reality that two sequences may only share limited regions of conserved sequence. Sometimes two sequences may be derived from ancient recombination events where only a single functional domain is ...
... Global algorithms are often not effective for highly diverged sequences - do not reflect the biological reality that two sequences may only share limited regions of conserved sequence. Sometimes two sequences may be derived from ancient recombination events where only a single functional domain is ...
Database Searches for similar sequences
... • blastp compares an amino acid query sequence against a protein sequence database • blastn compares a nucleotide query sequence against a nucleotide sequence database ...
... • blastp compares an amino acid query sequence against a protein sequence database • blastn compares a nucleotide query sequence against a nucleotide sequence database ...
Introduction to the GCG Wisconsin Package
... of new software by end users. Removes the need to learn new interface as new software is released. Provides a flow of analyses within a single ...
... of new software by end users. Removes the need to learn new interface as new software is released. Provides a flow of analyses within a single ...
Introduction to the GCG Wisconsin Package
... of new software by end users. Removes the need to learn new interface as new software is released. Provides a flow of analyses within a single ...
... of new software by end users. Removes the need to learn new interface as new software is released. Provides a flow of analyses within a single ...
Basic Phylogenetics and Tree Building
... • GLOBAL: Needleman-Wunsch-Gotoh algorithm • LOCAL: Smith-Waterman algorithm These have high algorithmic complexity (O(N2)), and are replaced by heuristic procedures in most practical applications. Most commonly used: BLAST family of algorithms (local alignment). ...
... • GLOBAL: Needleman-Wunsch-Gotoh algorithm • LOCAL: Smith-Waterman algorithm These have high algorithmic complexity (O(N2)), and are replaced by heuristic procedures in most practical applications. Most commonly used: BLAST family of algorithms (local alignment). ...
Genomewide Motif Recognition with a Dictionary Model
... words from an observed sequence. Moving from the same premises, we consider words that can be spelled in a variety of forms (hence accounting for varying degrees of conservation of the same motif across genome locations). The overall frequency of occurrence of each word in the sequence and the param ...
... words from an observed sequence. Moving from the same premises, we consider words that can be spelled in a variety of forms (hence accounting for varying degrees of conservation of the same motif across genome locations). The overall frequency of occurrence of each word in the sequence and the param ...
LEQ: How does RNA help to make a protein?
... The type of RNA that carriers the genetic information/message from DNA and coveys it to ribosomes where the information is translated into amino acid sequences ...
... The type of RNA that carriers the genetic information/message from DNA and coveys it to ribosomes where the information is translated into amino acid sequences ...
sal - RNA Informatics @ UGA
... – Next week, I will be attending the IMACS conference at UGA. I will also be presenting GAMSA (Genetic Algorithm for Multiple Stem Alignment) at the conference. – Building the RFAM 9.1 in a local copy of mySQL – Learning more about the RFAM database (which tables and attributes are useful to query f ...
... – Next week, I will be attending the IMACS conference at UGA. I will also be presenting GAMSA (Genetic Algorithm for Multiple Stem Alignment) at the conference. – Building the RFAM 9.1 in a local copy of mySQL – Learning more about the RFAM database (which tables and attributes are useful to query f ...
A Novel Method to Detect Identities in tRNA Genes Using Sequence
... We applied the method to Class I tRNAs to detect characteristic sites. We found that about 40% of characteristic sites that we detected are identities that have been detected experimentally, and that the remaining characteristic sites are in T and D domains which are the elbow regions of tRNAs. This ...
... We applied the method to Class I tRNAs to detect characteristic sites. We found that about 40% of characteristic sites that we detected are identities that have been detected experimentally, and that the remaining characteristic sites are in T and D domains which are the elbow regions of tRNAs. This ...
Dot plot - TeachLine
... statement which means “descent from a common ancestor” common 3D structure usually common function homology is all or nothing, you cannot say "50% homologous" ...
... statement which means “descent from a common ancestor” common 3D structure usually common function homology is all or nothing, you cannot say "50% homologous" ...
Cryptography and Linguistics of Macromolecules Cryptography and
... expressed in many forms: as a sequence profile that synthesizes the major commonalities between all sequences of the set, as a lattice that accounts for the possible compositions of sequence s, etc ...
... expressed in many forms: as a sequence profile that synthesizes the major commonalities between all sequences of the set, as a lattice that accounts for the possible compositions of sequence s, etc ...
Lesson 2 - Laboratory of Molecular Modelling
... (pairwise) or more (multiple) sequences. Searching for a series of identical or similar characters in the sequences. ...
... (pairwise) or more (multiple) sequences. Searching for a series of identical or similar characters in the sequences. ...
Sequence Alignment
... •Word Method - Multiple Alignment •Dynamic Programming •Progressive Methods •Iterative Methods •Motif Finding ...
... •Word Method - Multiple Alignment •Dynamic Programming •Progressive Methods •Iterative Methods •Motif Finding ...
Investigating Sequences - BioQUEST Curriculum Consortium
... BLAST databases (Plasmodium falciparum only, all Plasmodium ), genome maps, linkage markers, and information about genetic studies. Links are provided for other malaria web sites and genetic data on related apicomplexan parasites . ...
... BLAST databases (Plasmodium falciparum only, all Plasmodium ), genome maps, linkage markers, and information about genetic studies. Links are provided for other malaria web sites and genetic data on related apicomplexan parasites . ...
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.