Comment on "Extract fasta sequence from a multifasta file with fasta header Ids"
perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file If you have a large number of sequences that you want to extract, then you most likely have the sequence...1904 days ago
Comment on "Tools for Searching Repeats And Palindromic Sequences"
I wrote a tools "Palindromer" to find palindromes in whole genome sequences. You can try https://github.com/jnarayan81/Palindromer . I am happy to improve it, if any features are requested.2007 days ago
2117 days ago
2131 days ago
Comment on "Basic command-line to run BLAST"
...a_protein/mouse.protein.faNew DB title: mouse.protein.faSequence type: ProteinKeep MBits: TMaximum file size: 1000000000BAdding sequences from FASTA; added 76216 sequences in 2.87095 seconds.urbe@urbo2...2238 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...::208.871*9.76] mapped 120736 sequences[M::worker_pipeline::288.250*12.60] mapped 101108 sequences[M::worker_pipeline::370.153*1...:1043.026*17.99] mapped 62540 sequences[M::worker_pipeline::1120.649*...red 132126233 hits and 760720 sequences (8675939030 bp)[M::main] ===&...2275 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...of mapping. Skips self-hits if reads and reference files contain same sequences, and outputs lenient secondar...[false] --no-self-hits - Similar to overlapper, but skips mapping of sequences with same headers. Same seque...2286 days ago
2793 days ago
Comment on "Software packages for next gen sequence analysis"
DNAMAN uses fast alignment algorithms to assemble quickly and accurately a large number of overlapping sequences. This could be a nice tutorial for genome assemblies with overlapping sequences http://www.lynnon.com/pc/assembly.html3233 days ago
Comment on "Does anyone have Nanopore latest updates?"
...rchase any old, I mean current generation NGS sequencers, particularly the AMC warranty contracts after an year that will cost you more than the sequences coming out of the current gen...3267 days ago