List of SEALS programs

Note: system-dependent portions of the documentation are generated on the fly, so some sections of the static web documents may not agree with the documentation produced on your system.

man pages

gref

grefmatrix

grefre

rwidget

BLAST scripters

splat 

a BLAST scripter

• splatp wusplatp splatpgp
• splatn wusplatn splatngp
• splatx wusplatx splatxgp
• tsplatn twusplatn tsplatngp
• tsplatx twusplatx tsplatxgp

splish 

a BLAST scripter

• splishp wusplishp splishpgp
• splishn wusplishn splishngp
• splishx wusplishx splishxgp
• tsplishn twusplishn tsplishngp
• tsplishx twusplishx tsplishxgp

desplat 

clean up those messy splat searches

other scripters/wrappers

clustalify 

wrapper for ClustalW alignment/tree-building program

coilify 

wrapper for coils2 coiled-coil prediction by NCBI implementation

hmm_align 

wrapper for HMMER alignment programs

hmm_search 

database searches based on hidden markov models (wrapper for HMMer programs)

lupas_coilify 

wrapper for coils2 coiled-coil prediction by Lupas' implementation

phdify 

wrapper for PHD protein prediction

segify 

wrapper for SEG low-information domain detection

signalpify 

wrapper for signalP signal peptide prediction

BLAST result manipulation

blast2blast 

filter any kind of BLAST outputs by score, p : or e-value, etc.

blast2bounded 

extract HSPs / alignments from BLAST outputs

blast2gi 

convert BLAST results to lists or tables of hits

blast2filename 

convert BLAST results to lists or tables of hits

blast2header 

strip alignment/HSP data from BLAST files

gp2normal 

make gp variant outputs look more like old-style BLAST

psi2normal 

filter any kind of BLAST outputs by score, p : or e-value, etc.

shatterblast 

split/rename BLAST outputs according to query definition line

simple fasta file manipulation

assign_subversive_gis 

assign fake gi numbers to fasta records

columnize 

format fasta records into columns

daffy 

You must be taller than this script to ride this ride.

defkeys 

see the numbering of fasta defline fields

faand 

find the logical intersection between fasta libraries

faclean 

remove funny characters from fasta records

facount 

count the records in fasta libraries

fafilt 

filter out amino-acid or nucleic-acid sequences

faframe 

convert a nucleic acid sequence to various possible reading frames

faletters 

count the letters in fasta libraries

falower 

convert fasta records to lower case

faor 

find the logical union between fasta libraries

fanot 

find the logical difference between fasta libraries

fashuffle 

shuffle fasta records

fasort 

sort fasta libraries based on sequences or defline fields

fatweak 

tweak sequence boundaries

fauniq / nrify 

remove duplicate fasta records

faupper 

convert fasta records to upper case

faxor 

find the logical exclusive union between fasta libraries

fenestrate 

make windows on fasta records

gref 

match patterns in fasta libraries

mask_split 

split fasta records at masking boundaries

one2three 

convert single-letter amino acid codes to three-letter codes

remove_subversive_gis 

remove fake gi numbers from fasta records

select_defline 

select one of multiple deflines in fasta libraries

shatter 

split/rename fasta records based on the definition line

sieve 

remove long entries from fasta libraries

three2one 

convert three-letter amino acid codes to single-letter codes

GenBank flatfile manipulation

feature2fasta 

create fasta records from flatfile features

boundtable manipulation

blast2bounded 

extract HSPs / alignments from BLAST outputs

boundtable2fasta 

convert tables of sequence fragments into fasta libraries

compare_boundtable 

compare tables representing sequence fragments; find overlaps

merge_boundtable 

merge tables of sequence fragments

project_boundtable 

project normal and complement elements onto a single strand

split_boundtable 

split discontinuous sequence fragments

standardize_boundtable 

convert boundtables of different formats to the canonical SEALS format

strip_boundtable 

strip normal or complement elements from boundtables

Entrez retrieval

entrezping 

test your Entrez server

gi2abstract 

find abstracts associated with sequences

gi2fasta 

retrieve sequence data for a gi number

gi2genbank 

retrieve sequence data for a gi number

gi2asn1 

retrieve sequence data for a gi number

gi2defline 

retrieve sequence data for a gi number

gi2genbank_html 

retrieve sequence data for a gi number

genome2gi 

find all sequences from a systematic sequencing / mapping project

taxnode2amino_gi 

get all gis associated with a taxnode

taxnode2gi 

get all gis associated with a taxnode

taxnode2nucleic_gi 

get all gis associated with a taxnode

Netscape / html

hotbr 

html-ify BLAST outputs

hotgi 

hotlink gi numbers in any file

liftscape 

raise the current default Netscape window

peepscape 

grab the URL from a Netscape window

pipescape 

pipe a file into Netscape

pipescape_new 

pipe a file into Netscape

spitscape 

spit out the text from a Netscape window

pattern matching

gref 

match patterns in fasta libraries

grefd 

match patterns in fasta libraries

guess 

guess a pattern from an alignment

prosite2perl 

translates PROSITE-style regular expressions into Perl

prosite_as_perl 

search PROSITE by text word, returning perlish patterns

taxonomy analysis

tax_break 

summarize taxonomy data for a list of gi numbers

tax_collector 

summarize taxonomic identity of nearest homologs

tax_filt 

filter gi numbers according to taxonomy

tax_guess 

find an exact taxonomic name

tax_validate 

validate that the ranks in the taxonomy are consistent

taxnode2lineage 

see the lineage of any taxonomic node

unipred

coil_table 

create a table of predicted coiled-coil domains using ccp

seg_table 

create a table of predicted nonglobular domains using SEG

sig_table 

create a table of predicted signal peptides using SignalP

tm_table 

create a table of predicted transmembrane domains using PHD

unipred 

predict structural domains

general converters/extractors

boundtable2fasta 

convert tables of sequence fragments into fasta libraries

blastalign2fasta 

convert blast alignments to aligned fasta records

block2fasta 

convert aligned sequence blocks to aligned fasta records

clustalign2fasta / clustal2fasta 

convert CLUSTALW alignments into aligned fasta format

defline2gi 

extract gi numbers from the deflines of fasta records

fasta2clustalign 

convert aligned fasta records to CLUSTALW format.

fasta2defline 

extract the definition lines of fasta records

fasta2gi 

extract gi numbers from the deflines of fasta records

fasta2phylip 

convert aligned fasta records to PHYLIP format.

fasta2selex 

convert aligned fasta records to SELEX format.

fasta2seqrows 

convert fasta records to sequence rows

fastalign2fasta 

remove special delimiters from aligned fasta records.

fastalign2hmm 

convert aligned fasta records into a format compatible with HMMER

genbank2gi 

extract gi numbers from GenBank records

hmm2gi 

extract gi numbers from HMMER searches

hmmalign2fasta 

convert HMMER alignments into aligned fasta records

macaw2fasta 

convert MACAW alignments into aligned fasta format

most2gi 

extract gi numbers from MoST outputs

phylip2fasta 

convert PHYLIP alignments to aligned fasta records

selex2fasta 

convert SELEX alignments into aligned fasta format

seqrows2fasta 

convert sequences from sequence-row format to fasta records

miscellaneous functions

agree 

create a consensus sequence from an alignment

casealign2count 

substitute length values for unaligned regions in alignments

deindex 

cleans up index files created by fasta2index

fasta2index 

make indexes of fasta libraries for fast retrieval

famask 

mask fasta libraries based on predicted structural domains

gap_cds 

insert gaps in nucleotide sequence based on amino-acid alignments

gi2sibling 

find siblings for nucleotide and protein records

grouper 

group sequences by similarity scores

purger 

group sequences by similarity scores

wimklein 

a versatile translator

wubwub 

find duplications within a sequence

administration

seals 

examine your SEALS status

update_blastgp 

update BLAST-GP from the NCBI ftp site

update_gi_lists 

update retrieval hints from the NCBI ftp site

update_modules 

update Perl modules from a CPAN site

update_perlpath 

set the correct perl interpreter for SEALS scripts

update_permissions 

set permissions and links for your SEALS installation

update_prosite 

update the local PROSITE database from the Expasy web site

update_seg 

update SEG from the NCBI ftp site

update_taxonomy 

updates the local taxonomy databases from the NCBI ftp site

update_wublast 

update WU-BLAST from the Washington University ftp site

generic scripters

foreach_blast 

run a command on a series of BLAST results

foreach_fasta 

run a command on a series of fasta records

foreach_file 

run a command on a series of directories

foreach_genbank 

run a command on a series of GenBank-style flatfiles

foreach_dir 

run a command on a series of directories

foreach_line 

run a command on a series of lines

foreach_paragraph 

run a command on a series of empty line-delimited paragraphs

foreach_word 

run a command on a series of words

general utilities

bert 

a cat, with enormous globs

dupedupe 

find duplicate lines

mailme 

send a note to myself

nemp 

n e match print

pathadd 

add/remove path elements

plainwhich 

simple 'which' replacement

sortby 

sort lines according to a reference set

uniquniq 

create files of unique lines

singsing 

find unduplicated lines

stack_paragraphs 

stack paragraphs onto single lines

unstack_paragraphs 

unstack single lines into paragraphs

logical operations

and 

find the logical intersection between lines in files

not / nor 

find the logical difference between lines in files

or 

find the logical union between lines in files

xor 

find the logical exclusive union between lines in files

faand 

find the logical intersection between fasta libraries

fanot 

find the logical difference between fasta libraries

faor 

find the logical union between fasta libraries

faxor 

find the logical exclusive union between fasta libraries