M A F - Núcleo de Pesquisa Prof. Marcio Alves-Ferreira_____________________________________________



.NCBI Tools (BLAST and etc)	The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases, now comes in several types including PSI-BLAST, PHI-BLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences.
.EBI Tools (BLAST and etc)	The following are links to the various structural analysis tools we have available at the EBI.
.Clustal W	Clustal W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences
.MultiAlin	An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers
.TIGR Plant Transcript	TIGR Plant Transcript Assemblies represent clustered, assemblies of all transcripts for ~140 plant species and can be accessed here.
.CropNET	This site hosts a wide range of databases and software developed by UK CropNet, as well as hosting many other plant databases developed in the USA

.Interpro	InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
.Pfam	Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
.ProDom	ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
.COBBLER	COBBLER aligns a set of Blocks with a protein sequence and embeds a consensus representation of the Blocks in the sequence, which can then be used to search sequence databases using BLAST, and other sequence searching programs.
.BLOCKS	Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
.WoLF PSORT	WoLF PSORT predicts the subcellular localization sites of proteins based on their amino acid sequences. The method, which is a major extension to the venerable PSORTII program, makes predictions based on both known sortingsignal motifs and some correlative sequence features such as amino acid content.
.COGs	Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
.MEME - Multiple Em for Motif Elicitation	MEME will analyze your sequences for similarities among them and produce a description (motif) for each pat tern it discovers.