NEWS
2024-06-13
"Application of a new data management system to the study of the
gut microbiome of children who are small for their gestational
age" by Manske et al. has been uploaded to bioRxiv.
View
2024-06-07
"Interplay of miR-542, miR-126, miR-143 and miR-26b with PI3K-Akt
is a Diagnostic Signal and Putative Regulatory Target in
HPV-Positive Cervical Cancer" by Akram Rahimi-Moghaddam, Nassim
Ghorbanmehr, Sedigheh Gharbi, Fatemeh Nili and Eberhard Korsching
has been published by Biochemical Genetics
View
2023-08-28
"The complete sequence of a human Y chromosome” by T2T Consortium
has been published by Nature
View
2022-10-28
"The new uORFdb: integrating literature, sequence, and variation
data in a central hub for uORF research" by Felix Manske, Lynn Ogoniak,
Norbert Grundmann and Wojciech Makalowski has been published by
Nucleic Acids Research.
View
2022-07-08
"A Map of 3' DNA Transduction Variants Mediated by Non-LTR
Retroelements on 3202 Human Genomes" by Reza Halabian and Wojciech
Makalowski has been published by Biology.
View
2022-06
"paPAML: An Improved Computational Tool to Explore Selection
Pressure on Protein-Coding Sequences" by Lynn Ogoniak, Norbert
Grundmann and others
View
2022-05-14
"Mobilome of Apicomplexa Parasites" by Rodriguez and Makalowski
has been published by Genes.
View
2022-04-27
"Software evaluation for de novo detection of transposons" by
Rodriguez and Makalowski has been published by Mobile DNA.
View
2022-04-01
"From telomere to telomere: The transcriptional and epigenetic
state of human repeat elements" by T2T consortium has been
published by Science.
Goto
2022-02-12
"Global research alliance in infectious disease: a collaborative
effort to combat infectious diseases through dissemination of
portable sequencing" by GRAID consortium that IoB is part of has
been published by BMC Research Notes.
Goto
Main Databases
- PubMed - abstracts for 11 million biomedical articles
- Entrez - gateway to nucleotide and protein sequences
- LocusLink - curated sequence and gene descriptions
- PDB - 3D protein database at RCSB
- SwissProt - keyword search annotated protein collection
- SRS - query Swiss sequence retrieval system
- EBI SRS - query session at EBI sequence retrieval center
- EMBL - gateway to EMBL sequence and structure databases
- Hovergen - homologous vertebrate genes database
- HUGE - unidentified human proteins in KIAA series
- MIPS - gateway to protein information center in Munich
- OWL - non-redundant protein sequence database
- PIR - gateway to PIR protein database and query tools
- ChromList - lists UniGene clusters by chromosome
- ChromProt - lists human proteins by chromosome
- KEGG - Kyoto encyclopedia of pathways and maps
- Taxonomy - taxonomic classes at NCBI
- TreeLife - tree of life taxonomy project
- Hugo - recommended gene symbols at Genew3
- OMIM 1 and 2 - simple and complex searches at OMIM
- Marshfield - genetic and physical maps at Marshfield
- HGMD Mut - human gene mutation database at Cardiff
- LocMutations - locus-specific mutation databases
- Mitomap - human mitochondrial genome database
- Mito - mitochondrial genomes and alignment
- MitoWustl - mitochondrial genes, mutations and disorders
- MitoP - mitochondrial genes, proteins and diseases at Munich
- MitoDat - nuclear genes specifying mitochondrial biogenesis
- UDB - integrated human genome map
- UniGene - query UniGene
- UniGene HIB - annotated Unigene clusters and blast service
- Contigs - search NT contigs, dbSTS, GenMap99
- Marker - search for marker, YACs, contigs
- SNP - single nucleotide polymorphisms at SNP Consortium
- dbSNP - search for single nucleotide polymorphisms at NCBI
- BodyMap - database of human and mouse gene expression
- TransTerm - sequence context of stop and start codons
- ESTScan - detects coding regions despite frameshifts and low quality
- RegulonDB - transcription regulation database for various organisms
- Rebase - restriction enzyme cleavage sites
- SpliceDB - canonical and non-canonical splice sites in mammals
- MemTrans - genomic comparisons of membrane transport systems
- Geneimprint - imprinted gene database
- Codon - codon usage database
Genome Browsers & "Complete" Genomes
- Genome Browser - human genome assembly and track browser at UCSC
- Ensembl - human genome and disease gene browser at EBI/Sanger
- Map Viewer - human genome assembly and map viewer at NCBI
- Genome - query human genome and annotation database tables
- Download - download human genome and install mirror
- euGenes - five species map browser and 37,049 human gene reports
- Vista - visualization tool for long genomic alignments
- TIGR CMR - comprehensive microbial resource and genome browser
- NCBI - human and animal genome projects at NCBI
- Sanger - human genome project at Sanger Centre
- Jax - mouse genomics at Jackson Laboratory
- RatMap - rat genome database at Goteborg
- Zfin - zebrafish information network and database project
- Exofish - genome analysis of Tetraodon nigroviridis
- Flybase - database of drosophila genomics at Indiana
- BDGP - fruit fly genomics center at Berkeley
- WormBase - nematode mapping, sequencing and phenotypic repository
- ACeDB - genetics and genomics resource launcher
- SGD - yeast genome database
- TAIR - the arabidopsis information resource and tool center
- TIGR db - bacterial genomes at TIGR
- GOLD - monitors genome projects world-wide
- GenTotals - monitoring tables for genome progress
Gene Prediction and Feature Finding
- Mesquite: A modular system for evolutionary analysis
- Genscan D and M - identification of complete gene structures in genomic DNA
- GenomeScan - predicts genes incorporating protein homology
- RGD - comparative mapping tool for rat-mouse-humany synteny
- FGENEH - splice sites, coding exons, gene models, promotor and polyA
- Softberry - nucleotide sequence analysis, genes, promoters
- TwinScan - gene prediction for eukaryotic genomic sequences
- WebGene - ten tools for analysis of protein-coding gene structure
- Rosetta - predicts human coding exons based on homology
- GrailEXP - exons, genes, promoters, polyA, CpG islands at ORNL
- GeneWise2 - compares protein to genomic with introns and frameshifts
- Genie - finds multi-exon genes only, trained on human
- AAT - analysis and annotation tool for finding genes
- HMMgene - prediction of vertebrate and nematode genes
- NetGene2 - neural network predictions of splice sites
- GeneMark - gene prediction server at EBI
- GeneID - gene prediction of selected signals and exons
- RNAGenie - locates RNA genes from secondary structures
- Vienna RNA - seven RNA analysis tools
- Reverse Comp - reverse complement of DNA sequence
- McPromoter - finds eukaryotic RNA polymerase II transcription starts
- PromoterScan - predicts promoters using homologies with Pol II promoters
- ORF Finder - open reading frame finder for ORFs of cutoff size
- SeqTrans - identifies open reading frames in finished genomic
- Emboss - predict CpG islands and isochores
- UTR - untranslated regions of eukaryotic mRNAs
- AltSplice - database of alternate splicing in Ests and disease genes
- Webcutter - finds restriction endonuclease sites
- FSED - frameshift error detection in new sequences
- CheckSeq - uses homology to find coding regions and sequence errors
- ERR_WISE - detection of frameshift sequencing errors
- SEQERR - detection of frameshift error in coding regions
- MutCheck - transcription and translation effect of mutations
- Sift - predicts tolerated and untolerated protein substitutions
- TransFac - transcription factor database and tool collection
- MatInspector - searches for transcription factor binding sites
- VarSplice - collection of annotated splice variants
- TransPath - pathways in regulation of transcription factors
- TfScan - scans DNA sequences for transcription factors
- RepeatMasker - finds retroposons and repeats
- Censor - finds repeated elements, Repbase updates, maps
- Tandem - tandem repeat finder in DNA
- DotPlot - dot plot for internal DNA sequence repeats
- PatternHunter - finds approximate repeat patterns in genomic DNA
- TandemRepeats - finds adjacent imperfect repeat patterns in DNA
- Dst - finds human repeats and separated self-homology
- REPuter - genomic repeats of all types to 100kbp
- Tinoco - suggests secondary structure in RNA or DNA
- RNA_align - aligns two RNA species from secondary and tertiary structures
- REP - searches proteins for internal repeats
- Radar - detects and aligns protein repeats
- Repro - recognises repeats in a single protein query
Protein Tools and Browsers
- SwissTools - large collection of protein tools and databases
- Translate - translates DNA into 6 frames
- ReverseTrans 1 and 2 - reverse-translates protein into DNA
- SAPS - statistical analysis of protein sequences
- Emboss - peptide information and statistics
- Signalp - predicts signal peptide cleavage sites
- Psort - protein sorting signals
- TMpred - predicts transmembrane segments and orientation
- TMHMM - predicts transmembrane helices
- TopPred2 - topological prediction of membrane proteins
- TMAP - predicts membrane proteins from multiple alignment
- COILS 1 and 2 - prediction of coiled-coil regions in proteins
- PREDATOR - secondary structure from multiple sequences
- SSCP - predicts helix, strand and coil from composition
- STRIDE - secondary structure from atomic coordinates
- BCM SS - secondary structure by four methods
- Jpred - consensus method for secondary structure prediction
- TOPS - protein topology atlas and tool collection
- Interpro - integrated resource of protein families, domains and sites
- Pfam - alignments and hidden Markov models of protein domains
- SMART - simple modular architecture research tool
- ProDom - protein domain database
- ScanProsite - scans a sequence against PROSITE
- ProfileScan - scans sequence against profile databases
- FingerPRINTScan - search tool for Prints motifs
- ppsearch - pattern search tool for DNA or protein motifs
- HMMER - profile hidden Markov models for sequence analysis
- SAM - sequence alignment and modelling system by HMM
- BLOCKS - aligns ungapped segments of conserved protein regions
- IMPALA - blast search of BLOCKS conserved protein regions
- Blimps - improved BLOCKS search tool
- Motif - searches for motifs in query sequence
- FPS - family pairwise search library of protein families
- Cognitor - compare sequence to clusters of orthologous proteins
- Scop - structural classification of proteins
- SuperFamily - genomewide structural classification of proteins
- Pratt - search for conserved patterns in protein sequences
- Cath - hierarchical classification of protein domain structures
- MAST - motif alignment search tool
- MEME - analyzes protein and DNA for motifs
- Profam - curated protein classification and homology domains
- TIGRFAMs - protein families based on hidden Markov models
- ProtClass - protein classification browser
- Argos - protein surface and secondary structure tools
- Dali - coordinates of query compared to PDB database
- 123D - predicts tertiary structure
- 3Dee - database of protein domain definitions
- FSSP - fold classification based on structure
- PredProt - predicts protein structure
- PredictProt - threading, secondary, solvent and transmembrane
- Fold - 3D structures based on homologous sequences
- MaxSprout - protein backbone and side chains from alpha coordinates
- CE - finds structural alignments from PDB
- PQS - protein quaternary structure query form at EBI
- DIP - database of interacting proteins
- ProtFam - average core structures for families from structure
- SCWRL - sidechain placement using a rotamer library
- ASC - analytic surface calculation package
- AA Contacts - residue contacts, solvent accessibility
- ProStar - protein potential site
- Sweet - constructs 3D models of oligosaccharides from formula
- GlycoSuiteDB - curated relational database of glycan structures
- SwissPdbView - deep view for manipulation and analysis of PDB structures
- PBD Viewers - choices of plug-ins and 3D structure viewers
- Kinemages - interactive 3D protein web display
- RasMol - molecular visualization resource
- ProtExplorer - macromolecular viewer related to RasMol
- Chime - interactive web plug-in for 3D molecular structures
- Morph - downloadable protein shape morpher
- COMBOSA3D - combines alignment, protein 3D, and Chime to color
- Boxshade - pretty shading of multiple alignments
- ProtCol - tool for coloring proteins, default is by hydrophobicity
- ProtExpl - protein explorer interactive software
Family Specific
- GPCRDB - G-protein coupled receptor database
- NucleaRDB - nuclear receptors at UCSF
- NRR1 - nuclear receptor resource at Georgetown
- HORDE - human olfactory receptor genes
- GPCR - classifies G-protein coupled recepters
- Secator - classifies any protein family (receptors, tRNA synthetases)
- Merops - curated database on proteases
- Prion - annotated prion-doppel gene family
Blast, Blat, and Align Sequences
- Blast - java-free NCBI blast launch
- Swiss - blastp and tBlastn HTGS, UniGene at EMBnet
- Blast2 - restricts blast to user query and target
- BlastU - blast query against user fasta database
- Batch - batch blast from Baylor
- Blat - quick alignment of query to human genome assembly
- HumFin - blast finished human genome chromosome
- Mus 1 and 2 - blast finished mouse genome by chromosome
- Ensembl - blast human genome project
- Sanger - blast sequencing center chromosomes
- Traces - blast against raw new genomic trace reads
- SSAHA - trace server at Ensembl
- Hunt - search human novel transcript cDNAs
- WABA - genomic to genomic comparisons
- Pipmaker - percent identity plot alignment of two genomic sequences
- DBA - aligns two sequences sharing conserved blocks
- Alfresco - comparative genome sequence analysis
- ClustalW - aligns multiple sequences
- MAlign - aligns multiple sequences with flexible formatting
- Lalign - find multiple matching subsegments in two sequences
- Consensus - calculates consensus to ClustalW alginment
- Fasta3 - fasta3 alignment of protein sequence
- SnpFasta3 - alignment to HgBase SNP consortium
- MPsrch - alignment tool with many parameter controls
- Scanps - multi-alignment of query protein sequence
Tools Collections
- NHGRI and EBI and NCBI --"Genome Hub" pages
- NCBI - site map to extensive services
- BCM - launches numerous nucleotide and protein tools
- CMS - extensive directory of tools by category
- ABI - very large French tool compilation
- NAR - curated tool collection at Nucleic Acid Research
- UCSD - genome analysis by task area
- Workbench - unified area for searching and analysis
- EMBL1 - collection of database searching and tools
- EMBL2 - various EMBL alignment tools
- UCSF1 and 2 collections of tool links at UCSF
- MDC - bioinformatics tools at Delbruck Center
- EBI - tool and utility collection at EBI
- SDSC - tools at San Diego Supercomputer Center
- Bork - ten tool server of Bork lab
- Biocatalog - bioinformatic software collection
- MIA - search agent finds macromolecular information
- Phylip - tools and software for phylogenies
- Phylo - provides 14 utilties for phylogenetic analysis
- PAML - maximum likelihood of evolutionary parameters and hylogenies
- Stothard - The Sequence Manipulation Suite
Journals, Alerts, and General Internet
- PubMedJB - journal browser allows access to current issues
- Pubcrawler - provides alerts to new abstracts at PubMed
- HiWire - publishes online journals and provides alerts
- SeqAlert - provides daily homology sequence alerting
- New Issues - provides entry to 35 genomics jounals
- GenomeBio - free access to post-genomics journal, pre-print server
- PNAS - free access to month-old articles in PNAS
- JBC - nearly free access to most cited journal
- Science - high circulation general science journal
- Nature - gateway to restricted spin-off journals
- AmJHumGen - leading disease gene annotation journal
- Genomics - genomics articles sometimes stale
- GenomeRes - genomic research and methods articles
- Pedro - large journal (and tool) collection
- Web of Science - ISI web of knowledge
- OMD - online medical dictionary
- Google - best internet search site for web tools
- Lycos - widely used general search tool
- Yahoo - internet categories and news
- Nando - science and health news feed
- LangTrans - useful for rough translations between languages
2018-11-15 11:54
