RefSense is the name of both a web interface to PubMed, and a set of command line tools for accessing PubMed. RefSense provides easy access to PubMed’s data as well as some useful tools not found at the actual PubMed site.
RefSense allow you to search PubMed from a terminal (such as xterm), retrieve web pages or PDFs, find related articles, convert toBibTeX (convenient for LaTeX users), and much more by only using a keyboard. And you can get convenient word completion on titles, author names, etc, as well!
SIB-BLAST (Simple Is Beautiful) is a novel algorithm developed to overcome the model corruption problem that occurs frequently in the later iterations of PSI-BLAST searches.The algorithm compares resultant hits from iteration two and the final iteration of a PSI-BLAST search, calculates the figure of merit for each “overlapped” hit and re-ranks the hits according to their figure of merit. The premise of the algorithm is based on the observation that the profile, namely, the position specific scoring matrix (PSSM), in the first two rounds of a PSI-BLAST search, is the least corrupted since it is comprised mostly of close homologs. These profiles are used to search for more distant homologs, which are used to generate subsequent PSSMs. As more distant homologs are incorporated into the PSSM, non-homologous sequences frequently get included also, thus leading to model corruption. Hence, “benchmarking” hits from later iteration against earlier round when the model is least corrupted should improve the accuracy of a PSI-BLAST search.
Twease is a web-based tool to search Medline. Twease indexes each word of Medline, supports relevance or chronological searches, helps you find articles related to a set of articles of interest and provides many more features that can transparently expand your search to help find you the information you are looking for.
FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both, match/mismatch based and thermodynamic binding energy searches.
Seqool is a free (for educational use) sequence analysis software designed primarily for searching biological signals in nucleic acid sequences. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc.
Wang, M. 2011.
Seqool – A sequence analysis tool for signal search, pattern recognition and sequence statistics. Version 3.1,
available at: http://biossc.de/seqool.
MPtopoQuerier is a java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.
