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Spis dostępnych zasobów Internetowych

  1. Obszerny indeks dostepnych przez Internet usług.
  2. Spis oprogramowania (część z tych programów jest udostępniona przez rożne serwery internetowe).
  3. ExPASY Proteomics tools
  4. European Bioinformatics Institute  (EBI)
  5. Opis niektórych programow:

Identyfikacja białek na podstawie sekwencji aminokwasowej

AACompIdent

Description: Predicts the identity of a protein from its amino acid composition. It compares your experimental data with the Swiss-Prot database and matches the percent amino acid composition.

Input: Required input data include the amino acid composition of the protein being analyzed and the molecular weight and pI - if these parameters are known. Since few amino acid analysis methods provide information for all residues, specific constellations for groups of amino acids have already been indexed to facilitate this analysis.

 Results: Results are returned by email. Comparison of your protein with all of the proteins in the database results in a table of prospective proteins ranked according to their score. To facilitate identification, estimated molecular weight and pI of the proteins that best match your query sequence are provided.

[Additional documentation]

AACompSim

Description: Enables the detection of weak similarities between proteins by comparing amino acid compositions rather than sequences. The theoretical amino acid composition of a protein in the Swiss-Prot database is compared to all of the proteins in the database.

Input: Since few amino acid analysis methods provide information for all residues, specific constellations for groups of amino acids have already been indexed to facilitate this analysis. The analysis is initiated by selecting a constellation, then providing the SWISS-PROT ID or accession number (AC).

Results: AACompSim will return three lists of proteins with varied similarity to the query sequence. Results are returned by email, generally within 15 to 20 minutes.

[Additional documentation]

Restriction Enzyme Digests

Webcutter

Description: An excellent online tool that generates restriction maps of nucleotide sequences. It offers flexibility in an easy-to-use interface, and allows searching for the DNA sequence to analyze. Researchers choose to analyze the sequence as linear or circular, and Webcutter will find restriction sites that can be introduced by silent mutagenesis. Customization of restriction analysis is possible by clicking on a few radio buttons.

Input: There are three ways to input a nucleotide sequence - cut and paste, insertion of sequence from your local hard drive (this feature requires Netscape), or downloading one directly from NCBI's GenBank. An interface to GenBank enables searching the database and automatically entering the search results into Webcutter.

Results: Can be displayed as restriction maps or as tables ordered by enzyme or base pair number. One can choose to display all enzymes, non-cutters, single-cutters, or only those enzymes that cut at a specified number of sites. The "rainbow cutters" feature will display favorite enzymes in color or bold type, facilitating quick and easy ID.

PCR Primer Selection

 

Primer Selection

Description: This is the interface to xprimer, a tool for selecting sets of PCR primers for very large nucleotide sequences.

 Input: DNA sequences can be copied and pasted into the input window. Users select which "repeat database" and "genome model" to use, Tm range and size range for the primers.

Results: A table of viable forward and reverse primers are ranked and displayed, with the position for each of the primers on the query sequence included. The "image" version of this program graphically displays the location of the primers.

 

STS Pipeline Tool

Description: Designed to facilitate primer picking of short DNA sequences. It automatically strips away any specified vector sequences, scans for simple sequence repeats, conducts a FASTN search for highly repetitive sequences, and checks for possible duplicate sequences that may have been analyzed previously. In addition, BLASTn and BLASTx searches are conducted and a restriction site analysis completed on the sequence. Finally, pairs of primers are picked based on user-selected criteria.

Input: Nucleotide sequences are simply pasted in the input box Web site. Default values for all relevant parameters are already entered. Users have control over PCR product size, minimum, maximum and optimal Tm and primer size, and allowable ambiguous bases.

 Results: Results are returned by email as a formatted or raw report.

Tm Determination

Description: Tm enables one to select optimal DNA hybridization conditions and decide the minimum required length for DNA probes. The algorithm utilizes nearest-neighbor thermodynamic data to predict DNA duplex melting behavior from its primary sequence.

 Input: The DNA sequence is simply pasted in the input box. Sequences must contain at least one G or C and cannot be symmetric with a minimum length of 8 bases. Users can select both DNA and salt concentrations to refine the calculation.

Results: The calculated Tm is displayed within a few seconds.

Sequence Alignment Tools

 

Clustalw Multiple Alignment

Description: Clustalw utilizes sequence weighting and gap penalties to generate an optimized alignment for multiple sequences of nucleic acids or proteins. First, all sequences are compared to each other and a dendrogram describing the approximate sequence similarity groupings constructed. The final multiple sequence alignment is then completed using this dendrogram as a guide.

Input: Sequences to be aligned are input in Pearson/Fasta, Clustal, NBRF/PIR, EMBL/SWISSPROT, GCG/MSF or GDE formats. The program automatically determines the format used and whether or not the sequences submitted are DNA or protein. Pairwise alignment parameters affect the speed and sensitivity of the initial sequence alignments while parameters for multiple alignment affects the gaps introduced in the final sequence alignments.

 Results: Multiple sequence alignments are delivered by email and include optimized alignment as well as consensus sequences.

[Additional documentation]

 

Multalin Multiple Sequence Alignment

Description: Multalin is a multiple sequence alignment algorithm that utilizes progressive pairwise alignments. Several protein or nucleic acid sequences are arranged with gaps so that conserved bases or amino acid residues are aligned. A score is assigned for identity, conservative or nonconservative substitutions, and a penalty assigned to gaps. The program finds the optimal alignment by taking into account all possible alignments with the objective of maximizing the total score.

 Input: Sequences to be aligned are entered in Pearson/Fasta format.

 Results: Results of the multiple sequence alignment are delivered by email.

 

Protein Tools

 

DNA Sequence Translation

Description: This site identifies open reading frames (ORFs) for very large sequencing projects (e.g., yeast chromosomes). It includes a calculation of the codon adaptation index, which uses a reference set of expressed genes to assess and generate a score for a particular gene.

Input: Copy and paste a DNA sequence into the input box, or enter the GenBank Locus or sequence name.

 Results: Results are displayed on a Web page as a list of ORFs. It includes results of the translation in Fasta format, codon useage for each ORF and a codon adaptation index calculation.

PeptideMass

Description: Produces theoretical cleavage maps of protein sequences using a variety of enzymes. The molecular mass for each of the peptides generated is computed, as well as the theoretical isoelectric point.

 Input: Copy and paste the amino acid sequence as one-letter code into the input box. Post-translational modifications can be included in the analysis if known to occur on the query sequence. In addition, entries can be made with Swiss-Prot protein identifiers or accession numbers.

Results: Results are displayed on a Web page within a few seconds. A table of peptides generated is presented with relevant information such as molecular weight, peptide sequence and enzyme digest position within the query sequence.

 

ProtScale

Description: ProtScale is an excellent site providing researchers tools to compute and predict a profile produced by any amino acid sequence. Parameters include hydrophobicity and hydrophilicity estimates, secondary structure conformational parameters, molecular weight, bulkiness, polarity, refractivity, average flexibility, amino acid composition, average area buried, percent accessible and buried residues and HPLC retention data.

Input: Users can paste in an amino acid sequence. Alternatively, input methods include a Swiss-Prot/TREMBL accession number (AC) or a sequence identifier (ID).

 Results: Results are displayed on a Web page. Users can choose to display images in GIF or Postscript formats, or receive results in numerical formats.

SSPRED-Protein Secondary Structure Prediction

Description: The SSPRED Web site provides researchers with a tool that utilizes multiple sequence alignments to rapidly predict protein secondary structure. The protein that you wish to analyze must first be aligned to other structurally related proteins. Using this information, SSPRED completes a preliminary secondary structure prediction, then evaluates the accuracy of this computation relative to proteins with known three-dimensional structures.

 Input: Sequence files are submitted as a GCG multiple alignment sequence (msf file) or in the PIR format. Input must be initiated at the fill-out form.

Results: Results are delivered within minutes, in two email messages - one with the alignments and predicted secondary structure and a second containing secondary structure prediction with variable windows. The predicted structural elements are represented as 'H' for helical, 'E' for strand and 'C' for coil/loop.

Swiss-Model

Description: This is a protein modeling server that provides access to protein modeling tools via the Web. The program first finds all similarities of the sequence to be analyzed with sequences of known structure. Templates are selected with sequence identities over 25%, and used to facilitate modeling of the protein submitted.

 Input: The input required depends on the mode selected. The First Approach mode accepts sequences in RAW, Swiss-Prot, FASTA or GCG format. Alternatively, a Swiss-Prot AC code can be used in the submission. Sequence input for the Optimize mode is most easily completed by using the Swiss-PdbViewer.

Results: Results are delivered by email. Users can elect to receive results in Normal mode, which includes the final model coordinates file in PDB file format as well as a log of the analysis, the Swiss-PdbViewer mode which delivers the model as a project file for this viewer, or the Short mode which only returns the final model coordinates file.

Translate Tool

Description: Translates a DNA or RNA sequence into a protein sequence.

 Input: Copy and paste a DNA sequence into the input box.

 Results: Choose to display results in "verbose" or "compact" format. Several open reading frames (ORFs) are returned and users are prompted to select one of these. Once the frame is selected, a Swiss-Prot entry is automatically created from the methionine residue chosen to the first stop codon.

TMPred

Description: Predicts membrane-spanning regions as well as their orientations from query protein sequences. The program is based on a statistical analysis of Tmbase, a database of membrane-spanning proteins.

Input: Protein sequences can be copied and pasted into the input box as plain text, in readseq convertible formats (including SwissProt, Fasta, GCG and IG), SwissProt-ID or accession number, TREMBL ID or accession number or GenPept gi-identifier.

Results: The results of this analysis include possible transmembrane helices and suggested models on transmembrane toplogy. The predicted model can be received in GIF, postscript or numerical formats.

Math Tools

 

Visual Math

Description: Visual Math for Java 1.03 is an online graphic calculator and equation solver. Mathematical equations or systems of equations can be created with a variety of operators and functions. Solutions to these equations can be calculated and graphed. In addition, first- or second- order derivatives and integrals can be plotted by clicking on a menu.

Input: An equation is entered by copying and pasting text from your document, or by using the built-in function list.

Results: The equation entered will be solved for any intial value provided, and the function, derivatives and integrals of this function graphed.

Newton's Method

Description: Newton's Method is an iterative approach to finding the roots of a function, given an initial starting value. This Web site implements Newton's method through a simple interface, to find roots of the function you provide.

Input: To start, you must enter an expression using the available mathematical functions and constants supported by Java Script, and the first derivative of this function. An initial estimate for the root must be provided, as well as the number of iterations allowed.

Results: The Web site displays a table of results from each iteration in a separate browser window.

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