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The field of gene expression analysis continues to benefit from next-generation sequencing generated data, which enables transcripts to be measured with unmatched accuracy and resolution. But the high-throughput reads from these technologies also contain many errors, which can compromise the ability to accurately detect and quantify rare transcripts. Fortunately, techniques exist to ameliorate the affects of sequencer error. We present RecountDB, a secondary database derived from primary data in NCBI's short read archive. RecountDB holds sequence counts from RNA-seq and 5' capped transcription start site experiments, corrected and mapped to the relevant genome. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. The database is currently populated with 2265 entries from 45 organisms and continuously growing. RecountDB is publicly available at: http://recountdb.cbrc.jp.
Pubmed ID: 22139942
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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment.
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