How can I get the position of a short fasta sequence quickly?

[gejianye]

I am a new fellow on NGS. I really need some helps from your folks.

I have a short FASTA sequence (<100bp). I need to know which chromosome this sequence may locate at the human genome (for example this sequence locates at the chromosome 5. What software would be the best option? What command and arguments I need to use?

If I have a bunch of FASTA sequences and I need to obtain the same information. What software and commands I need to use?

Thank you so much!

[GenoMax]

As long as your query sequence is >40 bp blat may be the fastest way to identify targets.

If your list is small you may just want to use the web interface to blat here: https://genome.ucsc.edu/cgi-bin/hgBlat?command=start otherwise download and use the unix version locally (from the link above).

[Brian Bushnell]

The normal solution would be to use mapping, and there are numerous programs for this. For example, BBMap:

bbmap.sh in=queries.fasta ref=hg19.fasta out=mapped.sam nodisk -Xmx23g

The output will be in SAM format, documented here. If your computer does not have at least 24GB RAM, there are also other mapping programs that use less memory.

[gejianye]

Hi Brian,

Thank you so much for your reply.

I wonder if there is any other software available for Windows system. I guess BBMAP requires Linux?

And, which software programs requires less memory?

Thank you so much!

[Brian Bushnell]

Actually, BBMap works fine in Windows, just the shellscripts don't work so the command is a little different. If you only have a few sequences, you should try GenoMax's suggestion since it's web-based and will be faster for just a few sequences. But if you have a lot, it's easier to run a mapper against the whole file. In Windows:

1) Make sure you have Java installed. From a shell (which you get by executing cmd.exe), type "java -version". It should say something like this:

java version "1.7.0_60"
Java(TM) SE Runtime Environment (build 1.7.0_60-b19)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)

If nothing happens, or the version is older than 1.7.xxx, then you need to download Java from here
Run that executable.

2) Then, download and unzip BBMap. If it is in, for example, C:\bbmap\ then you would execute it like this:

java -ea -Xmx23g align2.BBMap in=queries.fasta ref=hg19.fasta out=mapped.sam nodisk

-Brian

P.S. Note that you will also need the human reference, hg19.fa, in a single file. You can get it here (you will need to extract that with a tool like 7-zip) or here (where it is already extracted). Both are as multiple files. If you can't find it as a single fasta file, you can apparently concatenate these in Windows using the type command.