### parallelized BLAT

###### Written by bonohu in misc on 火 01 5月 2018.

As I had to map assembled reads to the genomic sequence, I used BLAT (the BLAST-like Alignment Tool) for that purpose. BLAT was so fast for landing reads to genomic sequence, but it can be slow if reads are so many. I thought it would be so nice to have …

### SPARQLthon67

###### Written by bonohu in DBCLS on 金 27 4月 2018.

Joined SPARQLthon held at DBCLS Kashiwa. This was 67th SPARQLthon.

Discussed the development of two search systems (DBCLS SRA and AOE) and the integration of these. The specification will be fixed after the coming INSDC meeting of this year at NCBI.

I tried to add contents to how to make …

### Join files by key

###### Written by bonohu in shell on 日 25 3月 2018.

Joining two files by key in the first column of files can be easily done by using UNIX command below.

join -j 1 file1.txt file2.txt


This is very useful command, but the output is space-delimited by default. In order to get the output by tab-delimited, following option for …

### Retrieve a subset of sequence dataset

###### Written by bonohu in shell on 土 24 3月 2018.

In order to extract a set of sequence from FASTA-formatted file (both in nucleotides and peptides), several commands can be used to do so. In recent years, I regularly use blastdbcmd in NCBI BLAST suite. To run this command, the file must be indexed by makeblastdb with the option below …

When I want to count the number of redundant words in a file (hoge.txt), I have used simple Perl code like this(count.pl).