User talk:Darek Kedra

Pages to review:

• http://www.bioalgorithms.info/slides.php

• http://www.biomedcentral.com/1471-2105/7/499 (sequence alignment refinement paper)

• http://nar.oxfordjournals.org/cgi/content/full/33/22/7120 Automatic assessment of alignment quality

• ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL RASCAL 1.1

• http://www.dbi.tju.edu/dbi/index.php?menu=42 PAINT promoter database

• http://www.pdg.cnb.uam.es/fabascal/ tutorials ++

microarrays

• http://depts.washington.edu/l2l/ Database of up/down regulated genes

databases

• http://base.thep.lu.se/ BASE
• http://www.longhornarraydatabase.org/ LAD
• http://genome.tugraz.at/mars/mars_description.shtml MARS (2006) (doc HTML)
• http://www.sbeams.org/Microarray/ SBEAMS

overview [1]

Videos bioinformatics

• http://calit2.net/events/algorithmicbio/archive.php San Diego ALGORITHMIC BIOLOGY 2006

Positive selection

How to detect a pssitive selection of certain AA in a set of homologues sequences?:

• Selection (WEB) (requires >=5 ORFs + query ORF. Can handle PDB files
• SWAKK (WEB)
• SWAPSC (standalone Win and Linux) PHYLIP formated input

Sequence assembly

First generation

• phrap
• TIGR assembler
• CAP3 WWW@Pasteur

Genome assemblers used in current genomic projects

• Arachne @Broad Inst (largest number of citations)
• Phusion @Sanger
• Atlas @Baylor

• JAZZ -> @JGI in house only
• RAMEN (not published yet, used for medaka and silkworm projects)

New Programs

• Minimus suitable for bacterial genomes
• EULER P.Pevzner graph algorithm producing superior contigs

requires phrap and patched ReAligner

• MIRA Version 2.9.8 enables true hybrid sequence assembly (454 data with Sanger reads).

Mutation/SNP detection

• PolyScan ref New program claimed to be superior to MutationSurveyor/PolyPhred/SNPdetector

• MutationSurveyor $$$ program. 30 days demo available. MS3 has a limit of MS3 400 traces in a single project. GUI. Used in several diagnostic labs.

• novoSNP ref Windows/Linux 2.0.3. GUI & command line on Linux.

• SNPdetector (ftp) ref

• POLYBAYES Perl program. ref

• InSNP windows only, ABI base calls? detects substitution and indel SNPs in sequencing traces

• PolyPhred [ref http://nar.oxfordjournals.org/cgi/content/full/25/14/2745] 1997 program, integrated with phred and Consed.

ESTs clustering

Paper:

• EMBnet course (PDF)

Programs:

• Lucy2 standalone (Win Linux and MacOS)

Sequence assembly with ESTs enhancements=

• MIRA2 also detects SNPs

See also table with less frequently used algorithms: http://biolinfo.org/EST/assembly.htm

Alternative splicing

• ASTRA (Alternative Splicing and TRanscription Archives)
• ECgene Genome Annotation for Alternative Splicing. Large number of putative splice forms.

Sequence comparisons

Protein orthologues

• Exonerate tool from sanger
• Inparanoid

Genomic DNA

• PipMaker
• MultiPipMaker http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=168985

• GATA paper

GATA: a graphic alignment tool for comparative sequence analysis

Orthologues retrival

• OrthoMCL

Gene ontology

• Tutorials http://www.geneontology.org/GO.teaching.resources.shtml Very extensiive!

tutorials 2 check

• http://biophilessurf.info/tutorials.html

Genome annotation

• Jigsaw meta-program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models.

de novo predictions (eucariote, genomic level)

• Augustus

citation: http://genomebiology.com/2006/7/s1/S11

• GeneZilla

• Conrad java standalone

"""The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. The gene caller uses semi-Markov Conditional Random Fields. The Conrad CRF engineis a general purpose CRF engine used by the gene caller to provide the structure and algorithms for gene calling."""

To check: http://www.wormbase.org/wiki/index.php/NGASP To read: http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030054

syngr3

 	 RALGDS 2kb upstream

>chromosome:NCBI36:9:134962328:135016542:-1
TGGCCCCAGGAGGCTAGAGTTGGGGTATAGGGACCAGGTCACACAGGGTTCTGAATGCCA
GGCTAGGAGGCAGGGGTCACCGCAGGCCTGTCCCAGCAGGGGGATCAATATATATGGGGC
CCAAGCGCTGGACTCAGGGGATACCTGGCCAGCGAGGCCCCAACACAGGATGAGGCCTCT
GATGACCAGCTCGGGGATGAGTGACGGGGAAGAGCCATGAAGTGGGGGTCACCACGCACA
GCAGGGCCTGGCCACTTACAGCTGAGTGGCCTGCAGTGCTGGTGCCTTGGCTCTGGTATA
AAATTGAATGAAGCCGGGCACAGTGGCTCACGCCTGTAATTGCGGCACTTTGGGAGGCCA
AGGCAGGAGGATCTCTGGAGCCCAAGAGTTCCAAACCAGCCTGGGCAACATAGTGAGACT
TCATCTCTACATAGTTTTTTTAAAAATAAAAAAGGCCGGGCACAGTGGCTCACGCCTGTA
ATCCCAGCACTTTGGGAGGCCAAGGTGGGCAGATTACGAGGTCAGAAGTTCCAGACCAGC
CTGGCCAACATAGTGAAACCCCGCCTCTACTAAAAATACAAAAATTAGCCGGGTGTGATG
GCACATGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGACGGGAGAATCACTTGAACCTGG
GAGGTGGAGGTTGCAGTGAGCTGAGACTGTGCCATTGCACTCCAGTCTGGGTGACAGAGT
GAGACTCTGTCTCAAAAAAATAAAATAAATAAATAAATCAAAAGGGTTGGCCAGGCAAAG
TGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCGAGGAGGGCAGATCACCTGAGGTC
AGAAGTTCGAGACCAGCCTGGCCAATATGGTGAAACTCTGTCTCTACTAAAAACACAAAA
ATTAGTCGGGCGTGGTGGTGGCAGCGTGCACCTGTAATCCCAGCTACTTGGGAGGCTGAG
ACAGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAATAAGCCGTGATCTAGCCACTG
CATTCCAGCCTGGTCGACAAGAAGGAGACTGCGGCTGGTGCAGTGGCTCATGCCTGTAAT
CCCAGCACTTTGGGAGGCCAAGGTGGGAGGATCACCTGACGTCTGGAGTTTGAGACCAGC
CTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCGTGGTGG
CAGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGG
ACGTGGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCCAGCCTGGGGGACAAGAGT
GAGACTTCGTCTCAAAAAACAAACAAACGAGACTCCATCTCAAAAACAAAAGTAAATAAA
AAATAAAAAGGGACGAAATCAGTTAGCCCTAATAACACTGACTACCCCCAACAGTCGCTC
AACCCCAGTGTGAGGCCTCCTTCCCCCAGGCTCCCTTGAGCCCCATCTTACACCAGCTGA
AGCTGCAGCTGGACCTTGTGGTCCCGGGTGCTGTCAGGGAAGACAAGGAGGGAGGTGGGG
AAGAGGAGGGGAAGGGGAGACCTGACTTTCTCCCTGCCCAGGCTGAGTTCGCTGTCACCT
CGGGTCCCCCAGCTCCCAGCCATCCGCCGAGCCGAGTCCAGCAGGTGGCATCGGGGTGCT
GGGCGCCAGGGTGAACGTGTATATTTGGTGACGCCGGCGCGCCGACTCAGCGGCCCCCGC
CTGGCTGGGGCGAGGTTGGCCCTAGGTCCTAGCGGGGTGGGGAGTACTGAGCAGGCGGCT
GGGGCGGACGGACACGTGAGATCGGCCGCACATGGCGCTGGGAGCGTGGCGCGTGCGCGC
GGCGAAGCGGAGTGACGTGCACGCGCTGTCTGCGGTCCCGCGCAGGCCCCGTGTGCGCGC
CCGGCCTTGGACAACAGGCCCGGCTGCCCCGCGGGGGGAACACCCGCGTCGGCCCGCGGG
AGGGAGGCCTGAGCGCGCCCCCGAGCGCGTCCCCGAGCTCACGCGGCGGGGCGCGCCCCT
CGCACCTGCGGGCGGGCTGGGGCGGGGCCGCGGCTGTCCCCGCCCACCCGGGCCCGAGCC
CGGGGAGCCGGGGCGGAACCGAGCGGCGAGGCCCGAGCGGCCGGAGCGCGGCGCGGCGCA
GACAATGGGAGCGGCGCTGGCGGCTGCCGGGGCGGCCCCGAGGGCCGCAGAGTCCTGGGC
CCGGCGGGGACCGGAGGCCGCGCCATGAGCCCCGCAGCCGGGCGCACCCCTGCGCCGCGC
GCGGGCCCAGGCGAGCGGCCTCTGCGAGCCCCGGGTCCCGCCCTGGGGCCGGCGATGTGC
CACCGAGGCTGAGGATGATGGTAGATTGCCAG

Pathways

CPath

Blast tabulated output

Columns:

• Identity of query sequence
• Identity of subject sequence (matching sequence in database)
• Percent identity
• Alignment length
• Number of mismatches
• Number of gaps
• Start of query sequence
• End of query sequence
• Start of subject sequence
• End of subject sequence
• E-value
• Bit-score

Phylogeny

tree checks

• CONSEL

CONSEL: for assessing the confidence of phylogenetic tree selection Hidetoshi Shimodaira and Masami Hasegawa http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1246

• for clusters: PVCLUST R package

http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1540

tree builders

• BioNJ (NJ trees -> same speed better accuracy for large number of taxa)

alignments

• PANDIT database of multiple sequence alignments and phylogenetic trees covering many common protein domains.

genome variants DB

• TCAG curated catalogue of structural variation in the human genome

stuff to incorporate

• http://en.wikipedia.org/wiki/User:Darked/ABRF_2005

Protein vs mRNA level differences

Protein vs mRNA level deifferences

Stability of mRNA

• Decapping of mRNA
• Deandenylation

Regulation of translation

• number of ribbosomes per mRNA transcript
• binding of specific RBP (RNA binding proteins) to mRNA

Graph visualisation

• [Cytoscape http://www.cytoscape.org/]
• ONDEX

EST 2 genome alignment

• PALMA

ref

Portugal

• courses to check

motifs again...

• FOOTER paper web: http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php

chip-chip

• Ringo (R package): http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1906858

check: mpeak [4], TiMAT http://bdtnp.lbl.gov/TiMAT, MAT [5], TileMap [6], ACME [7], HGMM [8], and ChIPOTle [9]

Mass spec progs + sites

• http://proteome.gs.washington.edu/
• MyriMatch http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2007/6/i02/abs/pr0604054.html
• MyriMatch http://www.mc.vanderbilt.edu/msrc/bioinformatics/