blast
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blast对于reverse complement序列的支持
Understanding BLAST and Reverse Complementary RNA, and Discussing miRcore’s Future Leadership – miRcore.pdf
blast似乎用的这个数据库
http://www.lmdb.tech/doc/安装：
For get_species_taxids.sh
⚬ E-Direct: https://dataguide.nlm.nih.gov/edirect/install.htmlperl -MNet::FTP -e \ '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.tar.gz");' gunzip -c edirect.tar.gz | tar xf - export PATH=$PATH:$HOME/edirect"${PATH}:$HOME/edirect" sudo apt install libxml-simple-perl sudo apt --fix-broken install libio-socket-ssl-perl libnet-ssleay-perl perl-openssl-abi-1.1 ./edirect/setup.sh• For update_blastdb.pl
⚬ Perl: https://www.perl.org/将blast db导入到ES:
https://bitbucket.org/hspsdb/hspsdb-indexer/src/master/
不知道ES可否能做类似的相似搜索 -
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https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/blast/
blast的数据库格式:
nhr is the header file,
nin is the index file,
nsq is the sequence file
https://www.biostars.org/p/111501/ -
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http://sequenceserver.com
一个界面更友好的blast -
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BLASTn (Nucleotide BLAST): compares one or more nucleotide query sequences to a subject nucleotide sequence or a database of nucleotide sequences. This is useful when trying to determine the evolutionary relationships among different organisms (see Comparing two or more sequences below).
BLASTx (translated nucleotide sequence searched against protein sequences): compares a nucleotide query sequence that is translated in six reading frames (resulting in six protein sequences) against a database of protein sequences. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence.
tBLASTn (protein sequence searched against translated nucleotide sequences): compares a protein query sequence against the six-frame translations of a database of nucleotide sequences. Tblastn is useful for finding homologous protein coding regions in unannotated nucleotide sequences such as expressed sequence tags (ESTs) and draft genome records (HTG), located in the BLAST databases est and htgs, respectively. ESTs are short, single-read cDNA sequences. They comprise the largest pool of sequence data for many organisms and contain portions of transcripts from many uncharacterized genes. Since ESTs have no annotated coding sequences, there are no corresponding protein translations in the BLAST protein databases. Hence a tblastn search is the only way to search for these potential coding regions at the protein level. The HTG sequences, draft sequences from various genome projects or large genomic clones, are another large source of unannotated coding regions.
BLASTp (Protein BLAST): compares one or more protein query sequences to a subject protein sequence or a database of protein sequences. This is useful when trying to identify a protein (see From sequence to protein and gene below). -
https://www.ncbi.nlm.nih.gov/books/NBK279688/
Building a BLAST database with your (local) sequences$ makeblastdb -in test.fsa -parse_seqids -blastdb_version 5 -taxid_map test_map.txt -title "Cookbook demo" -dbtype prot -
直接比较两个序列
blastn -query test.fasta -subject ac008901.fasta也可以把一个序列用makeblastdb做成数据库 然后查询
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