InterestingStuff
Analysisof
Yeast Gene Promoter Sequences - Using NCBI's MACAW multiple allignmentprogram
together with a 16-letter code to search for promoters of co-expressedgenes.
Genome Databases
Human Genome
IgHLocus
-
EVERYTHING you ever wanted to know about the heavy chain.
Genelist
on chromosome 14.
HumanChromosome
14 - Sequence of 14q32.33 cytogenic band that contains IgH.
ContainsIgG2
constant region very close to the 3' end.
Human GenomeResource
Guide
Human-Mouse HomologyResource
IgBLAST - Antibodygene
analysis
Mouse Genome
MouseGenome
Resource Page at NCBI
Mouse Genome Informatics-
Mouse BLAST, other progs
TIGR Mouse Gene Index -cDNA
library, similar to above
Comparison, Homology and Analysis Tools
ExPASy Tools
NCBI SiteMap
Sick Kids Bioinformatics
Regulatory Sequence Databases
Web Signal Scan
- great TRANSFAC search engine.
Gene Regulation - Contains
multiple regulatory element databases and tools. User: mmrkobrada, pass:
transfac
COMPEL
http://sullivan.bu.edu/~mfrith/tools.shtml
Pattern and profile searches
MACAW - Multiple AlignmentConstruction
& Analysis Workbench - Locating, analyzing, and editingblocks of localized
sequence similarity among multiple seqences and linking them into acomposite
multiple alignment.
TEIRESIAS-
Generate patterns from a collection off unaligned protein or DNA sequences;at
IBM
Gibbs-
Pattern matching algorythm
InterPro Scan-
Integrated search in PROSITE, Pfam andd PRINTS
ScanProsite-
Scans a sequence against PROSITE or a pattern against SWISS-PROT andTrEMBL
ProfileScan-
Scans a sequence against protein profiile databases (including PROSITE)
Frame-ProfileScan-
Scans a short DNA sequence against prootein profile databases (includingPROSITE)
Pfam HMM search; scans a sequence against the Pfam protein familiesdb
[At Washington Universityor
at SangerCentre]
FPAT - Regular expressionsearches
in protein databases
PRATT - Interactively generatesconserved
patterns from a series of unaligned proteins
PPSEARCH - Scans a sequenceagainst
PROSITE (allows a graphical output); at EBI
PROSITEscan
- Scans a sequence against PROSITE (allows mismatches); at PBIL
SMART - Simple ModularArchitecture
Research Tool; at EMBL
Hits - Relationships between proteinsequences
and motifs
Multiple Sequence Alignment
CLUSTALW [At EBI, PBIL,EMBnet-CHor
at MBS (MBSALIGNER)]
ALIGN - atGenestream
(IGH)
DIALIGN-
Multiple sequence alignment based on ssegment-to-segment comparison,at
University of Bielefeld, Germany
Match-Box-
at University of Namur, Belgium
MSA - at WashingtonUniversity
Multalin [At INRAor
at PBIL]
MUSCA-
Multiple sequence alignment using patttern discovery, at IBM
AMAS-
Analyse Multiply Aligned Sequences&nbssp;
Bork'salignment
tools - Various tools to enhance the results of multiplealignments
(including consensus building).
CINEMA-
Color Interactive Editor for Multiple Alignments
ESPript-
Tool to print a multiple alignment&nbssp;
plogo-
Sequence logos at CBS/Denmark
GENIO/logo-
Sequence logos at Stuttgart/Germany&nbbsp;
WebLogo-
Sequence logos at Cambridge/UK
Similarity searches
BLAST and WU-BLAST - Interfaces to various versions of the Basic LocalAlignment
Search Tool
BLASTat
EMBnet-CH/SIB/CSCS (Switzerland)
ExPASy Interfaceto
EMBnet-CH/SIB/CSCS BLAST
BLAST at NCBI
WU-BLASTat
Bork's group in EMBL (Heidelberg)
WU-BLAST and BLASTat
the EBI (Hinxton)
BLASTat
PBIL (Lyon)
DARWIN -Data
Analysis and Retrieval With Indexed Nucleotide & Peptide Sequences-
ETHH-Z
Bic ultra-fast rigorous (Smith/Waterman) similarity searches usingthe
Bioccelerator [At EBI,DKFZor
at Weizmann]
DeCypher II - Smith/Watermanor
FrameSearch search using the DeCypher hardware accelerator
Fasta3 - FASTA version3
at the EBI
FDF -Smith/Waterman
type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH
PropSearch; searches for structural homologs using a 'properties' approach[At
EMBL
or at Montpellier]
SAMBA - Systolic Acceleratorfor
Molecular Biological Applications
SAWTED-
Structure Assignment With Text Descripption
Scanps - Similarity searchesusing
Barton's algorithm
Frameshift
Genewise-
Compares a protein sequence to a genommic DNA sequence, allowing forintrons
and frameshifting errors
FSED - Frameshifterror
detection
Other
All-in-OneSeq
Analyzer - General workbench for sequence analysis. 30000 basepairs
maximum.
Java-Based MolecularWorkbench
- Squence format conversion, gell band size calculatior,lots of useful
stuff. Small sequence size only.
AbCheck - AntibodySequence
Test
The Biology WorkBench - Searchmany
popular protein and nucleic acid sequence databases. Database searchingis
integrated with access to a wide variety of analysis and modeling tools,all
within a point and click interface that eliminates file format compatibilityproblems.
User:
Marko Pass: mmmm
Tutorials
Algorithmsfor
Multiple Sequence Allignment
MultipleSequence
Allignment
MultipleSequence
Allignment
Links
YaleLinks
Site
Programs
SSHclient
Unix
Simplecommands
Finger, Write andTalk
Commands
Preliminary Research Design
Annotation of sequence and discussion of possible
comparative analyses
Summary of allignment programs to be used,
as well as the sequences selected
Sequence
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