Tips for routine tools

1.hmmer

convalign.py stockholm file.aln(file.fasta)

hmmbuild –amino file.hmm file.sth

hmmsearch -o file.hmm.hit –noali –nobias file.hmm targetPep.fasta

 

 

2.blast

短序列
psiblast -query AT4G13850.1 -db ../../../conservation/subject/AT4G13850.1 -out AT4G13850.1.out -num_iterations 3 -evalue 20000 -matrix PAM30 -comp_based_stats 0

psiblast -query $(basename $@) -db /data7T/mercu-b-backup/pu b-data/NCBI-NR/nr -out $@ -outfmt 0 -num_threads 8 -threshold 0.005 -eval ue 10 -max_target_seqs 1000 -num_iterations 10 -inclusion_ethresh 0.002

#file.fasta由clustralw等多序列比对软件生成

psiblast -in_msa file.fasta ../../../conservation/subject/AT4G13850.1 -out AT4G13850.1.out -num_iterations 3 -evalue 20000 -matrix PAM30 -comp_based_stats 0

#返回fasta格式的数据

blastdbcmd -entry NP_172083.1 -db /data7T/mercu-b-backup/pub-data/NCBI-NR/nr

#自定义输出格式

blastp -query 1PP2.L.fasta -db /data7T/mercu-b-backup/pub-data/NCBI-NR/nr -out 1PP2.L.fasta.out.0 -num_threads=8 -outfmt=’6 qseqid sseqid pident length slen evalue’

http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html

短序列 psiblast -query AT4G13850.1 -db ../../../conservation/subject/AT4G13850.1 -out AT4G13850.1.out -num_iterations 3 -evalue 20000 -matrix PAM30 -comp_based_stats 0

psiblast -query $(basename $@) -db /data7T/mercu-b-backup/pu b-data/NCBI-NR/nr -out $@ -outfmt 0 -num_threads 8 -threshold 0.005 -eval ue 10 -max_target_seqs 1000 -num_iterations 10 -inclusion_ethresh 0.002

#file.fasta由clustralw等多序列比对软件生成

psiblast -in_msa file.fasta ../../../conservation/subject/AT4G13850.1 -out AT4G13850.1.out -num_iterations 3 -evalue 20000 -matrix PAM30 -comp_based_stats 0

#返回fasta格式的数据

blastdbcmd -entry NP_172083.1 -db /data7T/mercu-b-backup/pub-data/NCBI-NR/nr

#自定义输出格式

blastp -query 1PP2.L.fasta -db /data7T/mercu-b-backup/pub-data/NCBI-NR/nr -out 1PP2.L.fasta.out.0 -num_threads=8 -outfmt=’6 qseqid sseqid pident length slen evalue’

http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html

3.meme  [http://meme.sdsc.edu/meme/doc/meme.html]

meme F1_MEF.macs_peaks.pv2000.bed.fa -dna -nmotifs 1000 -evt 0.001 -revcomp \
-mod anr -minsites 50 -maxsites 10000 \
-maxsize `cat F1_MEF.macs_peaks.pv2000.bed.fa | wc -c` \
-oc F1_MEF.macs_peaks.pv2000.meme

 

 

4.meme修改

mcast调用mhhmscan出现错误 sh: line 1: 11764 Aborted

FATAL: mhmmscan failed with exit status 134, command run was:

 

Revise：

run with another parameter –blocksize

 

$(cell).macs_peaks.pv2000.homer: $(cell).macs_peaks.pv2000.bed

findMotifsGenome.pl $< mm9 $@ -size given -p 6
pythonmail2.py $@ $@

$(cell).macs_peaks.pv2000.meme-fimo-uniprobe: $(cell).macs_peaks.pv2000.bed.fa
fimo –output-qthresh 0.1 –max-seq-length 2.5e8 \
–oc $@ –max-stored-scores 1000000000 \
~/soft/meme/db/motif_databases/uniprobe_mouse.meme $<
pythonmail2.py $@ $@
tail -n +2 $@/fimo.txt | cut -f 1 | sort | uniq -c | sed ‘s/^ *//’ \
| awk ‘BEGIN{OFS=”\t”;FS=” “;}{print \(2,\)1}’ | sort -k1,1 \

$@/fimo.txt.motif.pattern.cnt
join -a1 -t ‘ ‘ -o 2.2,1.2 \
$@/fimo.txt.motif.pattern.cnt $(uniprobe_tf) \
$@/fimo.txt.motif.tf.cnt
$(cell).macs_peaks.pv2000.meme-mcast-uniprobe: $(cell).macs_peaks.pv2000.bed.fa
mkdir -p $@
mhmm –type star –keep-unused –verbosity 2 \
/home/chentong/soft/meme/db/motif_databases/uniprobe_mouse.meme \
$@/uniprobe_mouse.meme.mhmm
mhmmscan –fancy –allow-weak-motifs –p-thresh 0.0005 \
–max-gap 50 –e-thresh 10 –eg-cost 1 \
–blocksize \
`gawk ‘{if(x<length()) x = length()}END{print x}’ $<` \
–verbosity 5 –pseudo-weight 4.0 \
$@/uniprobe_mouse.meme.mhmm $< \
$@/mcast.txt
mhmm2html $@/mcast.txt >$@/mcast.html
pythonmail2.py $@ $@

5.

6.

7.

8.

9.

10.

11.

12.

13.

14.

15.

16.

17.

18.

19.

20.