Bioinformatics - a beginners' guide

(prepared for the ICRO Course on plant molecular genetics, July 2001, by Fatima Cvrckova)

Introductory presentation from the course (PowerPoint file)

Outline of course tasks

(detailed descriptions including links can be reached from the outline)

A compilation of links

A much larger list of links (but not entirely up to date) can be found on my site.

Evolutionarily conserved mechanisms in plant cell morphogenesis - in silico approach

(presentation from the lecture part of the course as a large zip file and my Genome Biology paper on plant formins)

Tasks

The excersise exists in five "flavors" (A,B,C,D,E). After completing the tasks, discuss its results with those who performed a different variant - intertesting things may come out from the comparison. Of course, you are free to do more than your share of the list.

Detailed descriptions of tasks can be reached via the corresponding links. Tools you will need can be reached via the list of links at this page; recommended tools are marked by corresponding letters.

Basic sequence manipulation

Perform restriction site analysis and/or translation of a given DNA sequence. Get acquainted with basic sequence manipulation tools.

Sequence similarity searches and domain structure analysis

Find relatives of a given nucleotide or protein sequence and examine the domain structure of a protein using a variety of approaches (BLAST, FASTA, pattern search, SMART). Examine the protein sequence for putative localisation or degradation signals.

Gene building: searching for coding sequences in chromosomal DNA

Predict the exon-intron structure of a given chromosomal sequence; verify the result by comparison with cDNA sequences.

Construction and interpretation of a protein sequence alignment

Construct an alignment of given protein sequences using a manual or automated method and select regions that would be suitable for phylogenetic analysis. (Define conserved peptide patterns/motifs and use them in database searching.)

Go to detailed descriptions:

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Basic links

Basic Bioinformatic Sites, Database gateways etc.

Sequence and structure databases

Sequence retrieval

Protein families

Sequence analysis

DNA and RNA -specific tools (translation, restriction, patterns, repeats and motifs, splicing)
Protein - specific tools

Sequence alignment

Sequence homology and pattern searches

(Not only plant) genome projects + genomics resources

Bioinformatics software

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Full list of links

Basic Bioinformatic Sites, Database gateways etc.
BCM Search Launcher
BCM Sequence Utilities A,B,C,D,E
Stanford Genomic Resources
NCBI HomePage
Entrez
ExPASy Molecular Biology Server
EBI: Searches
Sequence and structure databases

Sequence retrieval

Entrez
EBI-SRS Sequence Retrieval System
SWISS-PROT
PIR-Web - The Protein Identification Resource

Protein families

Pfam : Home page (St. Louis)
SCOP: Structural Classification of Proteins

"Personal pages" of distinct families

The Myosin Home Page
Kinesin HomePage
Protein Kinase Resource

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Sequence analysis
CBS prediction servers
BOXSHADE server

DNA and RNA -specific tools

BCM: Gene Feature Searches
BCM Sequence Utilities A,B,C,D,E
Gene Finder

(Other) translation sites

ExPASy - Translate tool B,D
The Protein Machine B
DNA Sequence Translation (ALCES)
Nucleic Acid to Amino Acid Translation D

Restriction

Webcutter 2.0 A, C, E
CUTTER (USA) A, C,E

Patterns, repeats and motifs

Dot Plot (to itself) (ALCES)
MatInspector
PatScan

Splicing

WebGene Home Page B,E
New GENSCAN Web Server at MIT A, D
Gene Finder A.th. splicing A,D
Splicing at NetGene2 server B,E

Protein - specific tools

SMART - Simple Modular Architecture Research Tool A, C
SBASE

Biochemistry and localization

WWW PESTfind
SignalP server B
TMHMM - detection of transmembrane segments B

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Sequence alignment

CMBI CLUSTAL W C, E
NPS@ (Lyon, France): npsa_clustalw.html E
CINEMA - interactive multiple alignment editor
Consensus
MSA

Sequence homology and pattern searches

BLAST

NCBI BLAST Search A,B,C
BLASTula SERVER home page
Searching plant ESTs using BLASTN (TAIR) C
Arabidopsis BLAST (Minnesota)C

FASTA

FASTA at Infobiogen (France, French interface only)D
FASTA at NPS@ (France) (SwissProt only) D
FASTA subset search (Indiana)
BCM: Protein searches

Motifs/patterns searching

Motif/Pattern/Profile searches EMBL

Based on own motifs

ISREC PatternFind Server E
TAIR Pattern Matching E
Protein Motifs (ALCES)
PatScan

Based on motif databases

TFSEARCH
MatInspector
ISREC Frame-ProfileScan Server
ISREC ProfileScan Server D
ProClass Database Home
ProDom Database home D
GeneFIND Family Identification System Home
BLOCKS
PRINTS

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(Not only plant) genome projects + genomics resources

MIPS
Kyoto Encyclopedia of Genes and Genomes
Cold Spring Harbor Genome Analysis
TIGR: The Institute for Genome Research

Arabidopsis and other plants

TAIR (The Arabidopsis Information Resource)
AIMS: Arabidopsis Information Management System
Arabidopsis Genome Resource - Nottingham
Home/Dept of Plant Gene Research/Kazusa DNA Research Institute
A. thaliana Classical Genetic Map
Arabidopsis Links

Sequenced insertion sites in A.th.

NASC Insert sequence blast server
GeneTrap
SINS
Arabidopsis Transposon Tagging Database

Microarrays

Yale Microarray Database
Stanford Microarray Database
Virtual Library: Plant-Arrays: Databases
AFGC Website (clone searches)
AFGC Website (microarray data searches)

Bioinformatics software
MACAW(for excercises, use the local copy, not this link - this is download only)
PHYLIP Home Page
ACACLONE - home of Kjeld Olesen's pDraw and more