RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing.
News
  • 2.24 is available now (Sep 27, 2016)
  1. Fix a bug that may miss some reads in some cases.
  2. Add more sample usages when rapsearch is called.
  • 2.23 is available now (Apr 6, 2015)
  1. Fix a bug that may overwrite results while query files are huge.
  2. Fix a bug that may crash the program while aligning long sequences.
  3. Fix a bug that may give negative E-value while using '-s F' option.
  • 2.22 is available now (Oct 27, 2014)
  1. Fix a bug that may report incorrect reference positions of an alignment given a very long reference sequence.
    1. Note that alignment itself is correct but just the reported positions are off.
    2. Re-indexing database is required.
  • 2.21 is available now (Oct 15, 2014)
  1. Add an option to output E-value instead of log(E-value), which makes RAPSearch2 more friendly to BLAST users.
  2. Fix a bug which convert lower-case IDs to upper-case.
  3. Adjust the format of float point values in result files to make it more clear.
  • 2.20 is available now (Oct 07, 2014)
  1. Fix a bug which causes crash while indexing database.
  2. Fix a bug which doesn't correctly translate lower-case nt to aa.
  3. Add an option "f" to index database with full fasta headers in order to facilitate annotation.
  • 2.19 is available now (Jul 02, 2014)
  1. Add an alternative option "i" to report hits according to bit scores instead of log-evalues.
  • 2.18 is available now (May 19, 2014)
  1. Fix a bug that may stop alignment in low complex region.
  • 2.17 is available now (Apr 14, 2014)
  1. Add options for streaming input and output. It's easier to incorporate RAPSearch2 into the pipeline.
  • 2.16 is available now (Jan 21, 2014)
  1. Add an option to print hits in XML format
  • 2.15 is available now (Oct 31, 2013)
  • 2.14 is available now (Aug 29, 2013)
  • A new module for paired-end sequences is available now (Apr 18, 2013)
FAQ
How can I cite RAPSearch2?
  • Yongan Zhao, Haixu Tang and Yuzhen Ye. RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data. Bioinformatics 2012, 28 (1): 125-126
What's fast mode?
  • RAPSearch2 with fast mode uses greedy strategies to stop low-quality alignment extensions, such as seed length, number of mismatches in seeds, gap extension conditions, etc.
How to output results just like BLAST (with E-values listed)?
  • By default, rapsearch outputs log(E-value) along with each hit in the output file.
  • Users can use "-s f" to let rapsearch output E-values.
How to change the E-value threshold for outputing hits?
  • -e parameter allows users to change the E-value threshold
  • For example, if a user only wants to get hits with E-values of <= 1e-5, use "-e -5" (when -s is not set), or "-e 1e-5" (when -s is set to f).
SF Project Page
SF Download Page
Module for Paired-End Sequences