- Free Internet bookmark for Biochemistry, Biomedicine, Molecular Biology researchers.

Journal Search
PubMed (MedLine)   (New PebMed)

DNA Sequence Database
GeneBank (Entrez Browser) @NCBI  (New Entrez)
EMBL (SRS Browser) @EBI
DDBJ  (DNA Data Bank of Japan)

Species Specific Database
Arabidopsis
Beans
Caenorhabditis elegans
Chicken
Cotton
Cow
Dictyostelium discoideum
Dog
Dorsophila
Maize
Mosquito
Mouse
Pig
Rat
Rice
Saccharomyces cerevisiae
Sheep
Soya  (Home)
Trees
Zebra Fish

Human Specific Database
OMIM Online Mendelian Inheritance in Man @NCBI

Protein Sequence Database
Entrez @NCBI   (New Entrez System)
PIR
SWISS-PROT+TREMBL  (Another Server)

Pairwise Sequence Alignments
ALIGN
align @mips
BLAST 2
LALIGN
LAP2
LFASTA
SIM (protien only)
Wise (Email result only)

Multiple Sequence Alignments
BLOCK MAKER (Protein only)
CAP Sequence Assembly (DNA only) <-- not available (Another Server @France)
CINEMA2
Clustal W @EBI
Clustal W @BCM
DOTTER (software download)
MAP     @BCM
Match-Box (protein only Email result)
MEME 2.2 (only Email result)
MSA 2.1 (Protein only)
MultAlin
PIMA 1.4 (Protein only)   @BCM
SEG (software download)

Sequence Utilities
MultSRS Retrive Multiple Seqs in FASTA format using Acession Number from Tigem Net SRS database <-- not available
ReadSeq (Conversion Utilities) convers your sequence to other format
Reverse Complement (Conversion Utilities)
Reverse, Complement or Reverse & Complement  (JAVA Enable Browser required)
SEQUTI Conversion Utilities (JAVA Enable Browser required) @JoyceBioNetwork

Presentation Methods
ALSCRIPT Software for PC, Unix
Boxshade
MacBoxShade Software for Mac

Comparing sequences against a database
BLAST
BlastHome  @NCBI
                  @BCM
                  @JGC
                  @French
FASTA  @UK
             @ORNL U.S. <-- not available
             @French
BLITZ  (Sequence similarity search of the SwissProt Database)
BEAUTY  Nucleic Acid   @BCM
               Protein  @BCM

Contig Assembly
CAP  Contig Assembly Program for Sequence Fragment Alignment and Assembly <-- not available
         (Another Server @France)
GCG Software Package
Staden Software Package

Predicting Protein-coding Region
cDNA
Frameshift Error Detection
MaxORF (Java enable browser required) @Joyce BioNetwork
MBS translator@MBS DNA Seq to Peptide Seq
ORF finder a graphical analysis tool which finds all open reading frames
Translate Tool (DNA to protein translation) @ExPASy   <Mirror site @Taiwan>
Translation Machine @EBI DNA Seq to Peptide Seq
WebGene Tools for prediction and analysis of protein-coding gene structure (Italy)
Wise2(Genewise) (compares a protein sequence to a genomic DNA sequence)

Genomic DNA
GRAIL 1.3 @ORNL  

DNA Analysis
Restriction enzyme maps
EnzFinder restriction enzyme search engine @MBS
REBASE (restriction enzyme database)
RestrictionMapper It supports linear and circular molecules, provides several options for sorting and filtering the output, and can simulate a simultaneous digest with user selected enzymes.
Webcutter  an on-line tool for restriction mapping nucleotide sequences (Another Server @USA)

Promoters and other DNA control sites
HCPolyA   (Hamming Clustering Method) Poly-A Site Prediction @WebGene  
HCtata  Hamming Clustering Method for TATA signal prediction in Eukaryotic Genes
Human Core-Promoter Finder  @Cold Spring Harbor
MatInspector/TRANSFAC  Professional Version
NNPP (Promoter Prediction by Neural Network)
POLYAH   Recognition of 3'-end Cleavage & Poly-A Signals
PROMOTER SCAN I
PROMOTER SCAN II
TESS
TFSEARCH (Transcription Factor Search)

Exon, Intron prediction
CpG @WebGene CpG islands prediction
FEXH
Genie (A gene finder based on generalized hidden Markov Model)
HEXON
HSPL
MZEF (Human Internal Coding Exon Finder) @Cold Spring Harbor
NNSSP (Splice Site Prediction by Neural Network)
Repeat @WebGene Repeated elements mapping
RepeatMasker2  it screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions
SpliceView  Splicing signals prediction @WebGene  

Primer Analysis
Primer3 (old version)    Primer3 New version Primer Picker
Primer Selection (xprimer base)
Tm Determination @U. Minnesota

RNA secondary structure prediction
MFOLD  for PC (filename: pcfldsrc.uue)
             for Unix

Protein Sequence Database
Entrez @NCBI  (New Entrez)
PIR (Protein Infomation Resource)a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available
SWISS-PROT+TREMBL  (Another Server)

Protein Structure Database
CATH  (Protein structure classification dataabse)
Entrez @NCBI   (New Entrez)
HSSP
NRL-3D (Sequence structure database)The database is produced by PIR from sequence and annotation information extracted from the PDB of crystallographic structures.
PDB The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography & NMR.
PROSITE @ExPASy  <Mirror site @Taiwan>
SCOP Structure Classification of Protein

Protein Secondary Structure Prediction
COILS (Lupas-algorithm) Prediction of coiled coil regions in proteins
Multicoil  Prediction of two- and three-stranded coiled coils @MIT
nnPredict
Paircoil   Prediction of coiled coil regions in proteins (Berger's method)
PHDsec  (@PredictProtein) Prediction of transmembrane helix location and topology
PREDATOR  Protein secondary structure prediction from single or multiple sequences
PSA  @BioMolecular Engineering Research Center(BMERC)
PSSP / NNSSP  @BCM
PSSP / SSP  @BCM --->not available
SAPS  Statistical analysis of protein sequences
SOPM  Protein secondary structure prediction
SOPMA  Protein secondary structure prediction

Protein Tertiary Structure Prediction
SWISS_MODEL  An automated knowledge-based protein modelling server
CPHmodels  Automated neural-network based protein modelling server
3D-PSSM  Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information ie.Foldfit
SWEET  Constructing 3D models of saccharids from their sequences
Swiss-PdbViewer   A program to display, analyse and superimpose protein 3D structures

Homology Modeling
SWISS-Model

Threading Algorithms and Fold Recognition
123D  a program which combines substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence throught the set of structures
frsvr  @UCLA
ProFIT         <-- not available
THREADER2  (Software download)
TOPITS

Protein Function Prediction
Calculating Hydrophobicity Profiles
Drawchca   Draw an Hydrophobic Cluster Analysis plot of a protein sequence
Plot the Hydropathic Profile of a Protein
PortScale Amino acid scale representation @ExPASy 

Predicting Transmembrane Helices
PHDhtm  (@PredictProtein)
SOUSI   Prediction of transmembrane regions
TMAP  Transmembrane detection based on multiple sequence alignment
TMpred  Prediction of transmembrane regions and protein orientation

Leader Sequences and Protein Localization
PSORT  Prediction of protein sorting signals and localization sites
SignalP Prediction of signal peptide cleavage sites

Comparing a Protein Sequence against Motif and Profile Database
BLOCKS Query sequence comparison against the BLOCKS database of highly conserved regions of protein
MoST Software for Unix
MOTIF Searching Protein and Nucleic Acid Sequence Motifs @GenomeNet, Japan
MPsrch (Email result)
PatScan  a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
PatternFinder  Pattern search of SwissProt and GenPept databases @ISREC
Pfam Protein families database of alignments and HMMs, a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains
Pratt2.1 Pattern discovery tool @Pasteur Inst.
PRINTS database A compendium of protein fingerprints. (Fingerprint is a group of conserved motifs used to characterise a protein family)
PROBE Software for PC
ProDom database
ProfileScan Compare a sequence against PROSITE Motifs Database @ISREC
PROSITE @ExPASy  <Mirror site @Taiwan>

Protein Science Utilities
PIR-ALN (database of protein seq. alignments derived from sequences and annotation in the PIR Database.)
RESID @PIR (database of amino acids modification)
Compute pI/Mw tool  Compute the Theoretical pI and Molecular Weight of a Protein Sequence @ExPASy

MHC Peptide Binding Prediction
HLA Bind  Prediction of MHC type I (HLA) peptide binding
SYFPEITHI  Prediction of MHC type I and II peptide binding @SYFPEITHI