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"SSAHA: Sequence Search and Alignment by Hashing Algorithm\n\nSSAHA is a software tool for very fast matching and alignment of DNA sequences.\n\nIt achieves its fast search speed by converting sequence information into a 'hash table' data structure, which can then be searched very rapidly for matches. "

"SAM\n\nA SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. A BAM file (.bam) is the binary version of a SAM file. These formats are described on the SAM Tools web site: http://samtools.sourceforge.net.\n\nIndexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Specifically, a BAM index file should be named by appending ".bai" to the bam file name. A SAM index filename is created by appending ".sai". In both cases the index files must reside in the same directory as the BAM or SAM file. \n\nTools for sorting and indexing BAM files are available at the SAM Tools website referenced above. SAM files can be sorted and indexed using the igvtools package. \n\nChromosome names: Chromosome names must be consistent across all annotation and data files. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g. 1 and chr1 are equivalent).\n\nOne-based index: Start and end positions are identified using a one-based index. The end position is included. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence."

Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.\n\nMaq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch. At the assembling stage, maq calls the consensus based on a statistical model. It calls the base which maximizes the posterior probability and calculates a phred quality at each position along the consensus. Heterozygotes are also called in this process.

Dominating the Next Generation Sequencing data analysis challenge\n\nWe have overcome the challenge to analyze Next Generation Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.\nCLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

"SignalP 3.0 Server\n\nSignalP 3.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models.\n\nView the version history of this server. All the previous versions are available on line, for comparison and reference.\n\nNew paper about using SignalP and other protein subcellular localization prediction methods:\nLocating proteins in the cell using TargetP, SignalP, and related tools\nOlof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen\nNature Protocols 2, 953-971 (2007)."

"Description\n\nOligonucleotide design program for use with ABI PRISM® 7900HT and 7000 Sequence Detection Systems "

Phred\n\nThe phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

Partek Incorporated develops and globally markets high quality software for life sciences research. Partek Genomics Suite, our flagship software, provides innovative solutions for integrated genomics and is unique in supporting all microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA.

Velvet\nSequence assembler for very short reads\n\nCurrent version: 0.7.63\n\nManual in pdf format\n\nPublic Git URL: git clone git://github.com/dzerbino/velvet.git\n\nFor up-to-date info, you can consult and/or subscribe to the mailing list.

"Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms. The algorithms offered include: * MAS5 Statistical algorithm * Probe Logarithmic Intensity Error Estimation (PLIER) * Robust Multichip Analysis (RMA)"

"microPred standalone version: Currently the microPred program is available only for the linux (Redhat/Fedora) platform. * Perl and Java VM should be pre-installed. * Install and execute the microPred as follows: "

"Affymetrix has recently decided to provide their main GeneChip analysis software at no charge. This is the new "GeneChip Operating Software", GCOS, which folds the old "Micro Array Suite"(MAS) and "Micro DB" into a single program. Previously this program would have sold for something like $6000 a license. Currently it is free to download and can be run on PCs running Windows 2000. (It may also run on Windows XP machines--validation of the program under this Operating System is being done by Affymetrix.) This is a bold move on their part, but I'm convinced that it is a very clever one. Nevertheless, Affy is clearly quaking with fear over this decision and have not really made any great announcement of it that I'm aware of. Thus far to my mind, the killer application provided by GCOS is a scatter plot with fold-difference lines on it. Take any two chips from the same experiment and plot them against each other. You can click on any point and get the name of the gene and the signal strengths, etc. Further you can click and "Info" button and be taken to Affy's NetAffx site to see more information about the gene of interest. Of course, same as will other biological data, if you haven't done replicates you might be looking at random noise. But that caveat aside if you focus on the 10x or 30x fold changes where one of the signals is reasonably high (above 100 at least) you should gather a list of interesting genes that can be followed up. "

"TMHMM Server v. 2.0\nPrediction of transmembrane helices in proteins\n\nNOTE: You can submit many proteins at once in one fasta file. Please limit each submission to at most 4000 proteins. Please tick the 'One line per protein' option. Please leave time between each large submission. "

"Bring your expression data to life \nGeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context.\n\nDeveloped on avadis™ from Strand Life Sciences, GeneSpring GX is part of Agilent's GeneSpring Analysis Platform for systems-level research."