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Types of Tools
Lab samples
Production Sequencing Software
Sequence data Databases, Database Search Tools
Production Sequencing Software
used throughout the sequencing procedure from preparation of the DNA through to the finishing of clones.
Example: Sanger Centre,Shotgun Sequencing of typical human clone
Data collection Transfer to UNIX Gel image processing Sequence pre-processing DNA Fragment Assembly Editing Finishing Services Quality Control and Assesment
Databases
Swiss-Prot EMBLEntrezGDBGenBankGSDBPDB& more -- see links at:http://www.public.iastate.edu/~pedro/rt_1.html
Species-specific Databases
See: http://genetics.about.com for both: Non-human and human genome projects
Examples: PomBase is a compilation of data relating
to the organism Schizosaccharomyces pombe
Wormpep predicted proteins from the C. elegans genome sequencing project.
Annotation Tools
Annotation of sequences with info such as homologies to known genes, possible gene locations, gene signals such as promoters, etc.
Example: Genotator (Nomi Harris) -- developing a workbench for automatic sequence annotation and annotation viewing and editing. The goal is to run a series of sequence analysis tools and display the results in such a way that the various predictions can be compared, and researcher makes decision of what to include.
Database Software
ACEDB is an acronym for "A Caenorhabditis elegans DataBase". It can refer to a database and data concerning the nematode C. elegans, or to the database software alone.
Other groups may adapt existing, or create own. For example, David Hall’s workflow project at UGA for Neurospora
Gene Prediction
Caution: accuracy <= ~ 70%Good review: Snyder and Stormo,
(chapter 11 of the book Nucleic Acid and Protein Sequence Analysis: A Practical Approach, second edition, 1994. )
Gene Prediction
GRAIL(Xgrail, JavaGrail, etc.)GeneidNetgeneGenMarkFexon, Hexon GENSCANxpoundGenefinder (University of Washington)
GRAIL
Predicts coding regionsUses a neural network which combines a
series of coding prediction algorithms. recognizes coding potential within a fixed
size (100 base) window; evaluates coding potential without looking for additional features
later versions incorporate additional info human and other species
GeneMark
Based on inhomogeneous Markov models
predicts coding and non-coding regions based on statistical patterns in dinucleotide frequences … more next week from Mark B.
Pairwise Alignments
SIM (Protein only) - k best non-intersecting alignments (EXPASY)
ALIGN - optimal global alignment with no short-cuts (EERIE)
LALIGN - calculates the N-best local alignments (EERIE)
LFASTA - local similarity searches showing local alignments (EERIE)
BLAST 2 - local alignment using BLAST (NCBI) LAP2 - local DNA to protein alignment with LAP2 (MTU)
Multiple Sequence Alignments
ClustalW 1.7 (DNA/Protein) - Global progressive (BCM) CAP Sequence Assembly (DNA) - Contig Assembly MAP (DNA/Protein) - Global progressive in linear space PIMA 1.4 (Protein only) - Pattern-Induced (local) Multiple
Alignment (BCM) MSA 2.1 (Protein only) - Near-optimal sum-of-pairs global
(WashU) BLOCK MAKER (Protein only) - Finds conserved blocks in seq
sets (FHCRC)ClustalW 1.7 (DNA/Protein) - Global progressive (BCM)
MEME 2.2 (DNA/Protein) - Multiple EM for Motif Elicitation (SDSC)
Similarity Searching
BLAST -- (BLASTP, TBLASTN, etc.) a nucleotide or protein sequence sent to
the BLAST server is compared against and a summary of matches is returned to the user.
allows all combinations of DNA or protein query sequences with searches against DNA or protein databases:
BLAST variations
blastp compares an amino acid query sequence against a protein sequence database.
blastn compares a nucleotide query sequence against a nucleotide sequence database.
blastx compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
Protein Structure Prediction
Ab initio -- based on energy minimizationfold recognition -- sequence -> secondary
structure, then align secondary structures with corresponding secondary structures in related proteins, etc.
statistical -- based on “hidden patterns”; similar patterns -> similar structure
Protein Secondary Structure Prediction
Coils - prediction of coiled coil regions nnPredict - uses a 2 layer neural networkPSSP / SSP - segment-oriented predictionPSSP / NNSSP - nearest-neighbor prediction SAPS - statistical analysis of protein sequencesPaircoil - coiled coil regions of pairwise residue
correlationsProtein Hydrophilicity /HydrophobicitySOPM - self optimized prediction method
Protein Function Prediction
Pfam - groups of similar function proteins
aligned and HMMs generated for each “cluster”
HMM generated for unknown function protein and compared to HMMs of known proteins for predicted function classification
Pfam components
PROTEIN HMM SEARCH - Analyze a protein query sequence to find Pfam domain matches.
DNA HMM SEARCH - Analyze a DNA query sequence to find Pfam domain matches. (Uses the GeneWise server at the Sanger Centre.)
BROWSE PFAM - View Pfam annotation and alignments.
TEXT SEARCH - Query Pfam by keywords.
BROWSE SWISSPFAM - View the domain organization of any SWISSPROT/TrEMBL sequence according to Pfam.
Phylogeny Reconstruction
Construct evolutionary trees based on divergences that occur in related sequences parsimony, minimum distance, etc. parsimony -- construct tree so that
number of mutation events is minimized PHYLIP, PAUP, others, some interactive
Physical Mapping Software
used to physically locate genetic markers.
FPC Software for FingerPrinting Contigs.
Image 3.x Software for processing fingerprint gel images.
RHServer This web interface positions one or more markers on the 1998 International Gene Map (GB4).
SAM System for Assembling Markers. SAM takes as input a set of clones and their associated markers, and outputs a partially ordered marker map.
Z-RHMAPPER Extensions to the RHMAPPER (Whitehead) Radiation Hybrid Mapping Package.