Sequence Analysis
Sequence analysis tools
Homology & Similarity searches |
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| BLAST | Blast (Altschul et al., 1997) stands for Basic Local
Alignment Search Tool. The emphasis
of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about
the structure and function of your novel sequence. Read more |
| PSI-BLAST |
PSIBLAST, or Position-Specific Iterated BLAST, uses the methods described in Altschul, et al. Nucleic Acids Res. 25(17):3389-3402 (1997) and Schaffer, et al. Nucleic Acids Res. 29(14): 2994-3005 (2001) to search for similarities between protein query sequences and all the sequences in one or more protein databases. |
| FASTA | The FASTA packages ( W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448) contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. |
Multiple alignment |
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| CLUSTALW | Clustal W (Thompson et al., 1994) is a general purpose multiple alignment program for DNA or proteins. It can be used to produce a multiple alignment or a phylogenetic tree. Read more. |
| MUSCLE | Muscle (Edgar, 2004) is a computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function -- "the log-expectation score" -- and refinement using tree-dependent restricted partitioning. Read more. |
| TCOFFEE | Tcoffee (Notredame et al., 2000) is a collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of Protein Sequences and Structures. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can combine sequences and structures. Read more. |
RNA tools |
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| Vienna RNA Package | The Vienna RNA Package (Hofacker et al., 1994) consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA
secondary structures. Read more. |
EMBOSS |
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| water & needle |
Water: uses the Smith-Waterman algorithm (modified for speed
enhancments) to calculate the local alignment. Needle: uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length. Read more. |
| EMBOSS (Rice et al., 2000)is "The European Molecular Biology Open
Software Suite". EMBOSS is a free Open Source software analysis package
specially developed for the needs of the molecular biology (e.g.
EMBnet) user community. The software automatically copes with data in a
variety of formats and even allows transparent retrieval of sequence
data from the web. You can download the whole EMBOS Suite from our FTP server and install it on your own system. We will make available on the web those of the tools of EMBOSS that will be more often used. Read more. |
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