BETRAN LAB

Evolutionary Biology

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NUCLEIC ACIDS

DNA Sequence Homology Analysis & Searching

BLAST Basic Local Alignment Search Tool. BLAST2 Gapped BLAST. FASTA3 Sequence similarity and homology searching against nucleotide and protein database using Fasta3.

Protein Search Using a Nucleotide Sequence

Darwin Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences. SWsrch Programs

Gene Search Using a Protein Sequence

SWsrch Programs

DNA/RNA Structure & Function Analyses

Multi-Function Structure Analyses

THE MEME/MAST SYSTEM Multiple EM for Motif Elicitation. PatScan DNA Sequence Motif Analysis.

Poly-A Site Prediction

HCpolya Hamming Clustering poly-A prediction in Eukaryotic Genes

Exon (ORF)Prediction

Cassandra Recognition of Protein-Coding Segments. ETOPE Allows you to test biological validity of computationally predicted exons. FramePlot Protein Coding Region Prediction in Bacterial DNA.Gene Finder designed to predict putative internal protein coding exons in genomic DNA sequences. GENIE Gene [prediction] Finder. ORF Finder Open Reading Frame Finder. GeneMark Gene prediction service.Grail
Ultimate™ ORF Browser

Splice Site Prediction

NNSSP Splice site prediction by neural network.

Search/Prediction of Potential Splice Sites in DNA NetGene2 is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA. NetPlantGene is a service producing neural network predictions of splice sites in Arabidopsis thaliana DNA.

TATA Signaling, Promoter & Trans-Factor Bind Site Prediction

MatInspector Search Sequence for Transcription Factor Binding Sites.NNPP Promoter Prediction. WWW Signal Scan scans DNA sequences for eukaryotic transcriptional elements.Tfsitescan Promoter analysis.

Recognition of PolII Promoter Region & Transcription Start Signals Using

ProGA Eukaryotic Promoters Recognition by Genetic Algorithm Transfac 6.0 is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.

Repetitive DNA & CpG Isles Analyses

Grail, GrailEXP predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence. RepeatMasker2

Analysis of Repetitive Elements in DNA Sequences

tRNA Gene Prediction

tRNAscan Genomic tRNA Gene Identification.

Multi-Function Search & Data Retrieval Servers

ENTREZ Nucleotide Sequence Search.SRS7 Database searching using the Sequence Retrieval System version 7.

Nucleotide Sequence Alignment Servers

Bork's alignment tools Various tools to enhance the results of multiple alignments (including consensus building). LALIGN Calculates N-Best Local Alignments between Two Sequences. Multalin at INRA Multiple sequence alignment by Florence Corpet. MSA Multiple Sequence Alignments. ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.

Sequence Manipulation Tools

Sequence Orientation Conversion Utilities

ReadSeq Sequence Format Conversion Utility. Reverse, Complement or Reverse and Complement Sequence Orientation Conversion Tool. Reverse Translator Sequence Orientation Conversion Tool.

Restriction Enzyme Mapping Analysis

RE Finder, WebCutter, WWWtacg3

Translate a DNA Sequence into a Protein

6 Frame Translation Tool Translate DNA Sequence in all 6 Frames. Translate Tool Protein Translation. Transeq Translates DNA sequences.

Sequence Presentation/Publication Tools

BOXSHADE Printing and Shading of Multiple Sequence Alignments.

Miscellaneous Analyses

Chimera Server Determine if 16S rRNA Sequence is Chimeric.Poland Calculate the thermal denaturation profile of double stranded RNA or DNA.

DNA Sequence Databases & Search Engines

CpG islands Database Human Genes and Their Associated CpG Islands. dbEST Database of Expressed Sequence Tags.Search Link to dbEST Database, dbSTS Database of Sequence Tagged Sites. ePCR User query sequence search against STS primer sequences in dbSTS. DDBJ DNA Database of Japan.

DNA Cloning Vectors Sequence Database

Phage Vectors. VECTOR DATABASE. Redasoft Cloning Vector Search Engine.

EMBL Nucleotide Sequence Database The EMBL Nucleotide Sequence database is a comprehensive database of DNA and RNA sequences. DBGET Integrated Databases Sequence/ Information Retrieval Service. EMBL Search Search of EMBL Database. ENTREZ Nucleotide Database Search Server. GenBank DNA/Protein Sequence Database. BankIt Info on submitting sequences to GenBank.

HOVERGEN Vertebrate Genes Database. KEGG Search Gene Names in KEGG Pathway Database. Primer Selection Select primers in a Gene sequence.TBASE Transgenic/Targeted Mutation Database.

RNA Sequence Databases

5S ribosomal RNA home page 5S rRNA Sequence Database. Comparative RNA Web Site Introduction. Compilation of tRNA sequences and sequences of tRNA genes It contains sequences of tRNAs and tRNA genes. European ribosomal RNA database. Non-coding RNA database. PLMItRNA Compilation of higher plant mitochondrial tRNA genes.uRNA Database The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Ribosomal Database Project. RNA Editing Web Site. RNA World. RNase P Database (Microbiology, NCSU) . Signal Recognition Particle Database. Small RNA database at Baylor. SnoRNA database. tmRNA Database. UTR 5' AND 3' mRNA untranslated regions databases. Yeast snoRNA database.

Multi-Database Search & Retrieval Tools

DBGET Integrated Databases Sequence/Information Retrieval Service. ENTREZ Nucleotide Database Search Server.

Gene Expression & Translation:cis-Elements & trans-Acting Factors

Transcription Factors/Elements Databases

ooTFD Transcription Factors Database. TRANSFAC Transcription Factor Database. TRRD Database of Transcription Regulatory Regions.

Transcriptional Regulation- Information

amdS Gene Regulation.

Translational Signals/Elements

TransTerm A Translational Signal Database.

Standard & Organism-Specific Codon Tables

Organism-Specific Codon Tables

Codon Usage Database Standard Codons for Nuclear Genes Standard Eukaryotic Codon Translation tables (CTT).

DNA Restriction Enzyme Databases

ReBase Restriction Enzyme Database.

Other Species

Pristionchus Sequence Database
The Neurospora Genome Project
The Schizosaccharomyces pombe Genome Sequencing Project


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